The following railroads currently or formerly operated in the U.S. state of New York.
| Name | Mark | System[1] | From | To | Successor | Notes | | Addison Railroad | RUT | 1867 | 1951 | N/A |
| Addison and Northern Pennsylvania Railway | B&O | 1882 | 1887 | Addison and Pennsylvania Railway |
| Addison and Pennsylvania Railway | B&O | 1887 | 1898 | Addison and Susquehanna Railroad |
| Addison and Susquehanna Railroad | B&O | 1898 | 1954 | Buffalo and Susquehanna Railroad |
| Adirondack Company | D&H | 1863 | 1882 | Adirondack Railway |
| Adirondack Railway | D&H | 1882 | 1902 | Delaware and Hudson Company |
| Adirondack Railway | ADIR | 1976 | 1981 |
| Adirondac Estate and Railroad Company | D&H | 1860 | 1863 | Adirondack Company |
| Adirondack and St. Lawrence Railroad | 1906 | 1925 | N/A |
| Albany and Hudson Railway and Power Company | 1899 | 1903 | Albany and Hudson Railroad | Electrified in 1900 |
| Albany Northern Railroad | D&H | 1851 | 1856 | Albany, Vermont and Canada Railroad |
| Albany and Schenectady Railroad | NYC | 1847 | 1853 | New York Central Railroad |
| Albany and Susquehanna Railroad | D&H | 1851 | 1945 | Delaware and Hudson Railroad |
| Albany and Vermont Railroad | D&H | 1859 | |
| Albany, Vermont and Canada Railroad | D&H | 1856 | 1859 | Albany and Vermont Railroad |
| Albany and West Stockbridge Railroad | NYC | 1836 | 1870 | Boston and Albany Railroad |
| Allegany Central Railroad | PS&N | 1881 | 1883 | Lackawanna and Pittsburgh Railroad |
| Amsterdam, Chuctanunda and Northern Railroad | NYC | 1879 | |
| Atlantic Avenue Railroad | LIRR | 1872 | 1899 | Nassau Electric Railroad | Main line operated by Long Island Rail Road under a 99-year lease from 1877 |
| Atlantic and Great Western Railroad | ERIE | 1871 | 1880 | New York, Pennsylvania and Ohio Railroad |
| Atlantic and Great Western Railroad | ERIE | 1859 | 1865 | Atlantic and Great Western Railway |
| Atlantic and Great Western Railway | ERIE | 1865 | 1871 | Atlantic and Great Western Railroad |
| Attica and Allegheny Valley Railroad | 1852 | 1856 | Attica and Arcade Railroad |
| Attica and Buffalo Railroad | NYC | 1836 | 1850 | Buffalo and Rochester Railroad |
| Attica and Arcade Railroad | 1870 | 1880 | Tonawanda Valley Railroad |
| Attica and Freedom Railroad | 1891 | 1894 | Buffalo, Attica and Arcade Railroad |
| Attica and Hornellsville Railroad | ERIE | 1845 | 1851 | Buffalo and New York City Railroad |
| Auburn and Ithaca Railway | LV | 1889 | 1890 | Geneva and Van Ettenville Railway |
| Auburn and Rochester Railroad | NYC | 1836 | 1850 | Rochester and Syracuse Railroad |
| Auburn and Syracuse Railroad | NYC | 1834 | 1850 | Rochester and Syracuse Railroad |
| Avon, Geneseo and Mount Morris Railroad | ERIE | 1860 | 1940 | N/A |
| Baltimore and Ohio Railroad | B&O, BO | B&O | 1932 | 1987 | Chesapeake and Ohio Railway |
| Bath and Hammondsport Railroad | BH | 1872 | 1993 | Champagne Railroad |
| Battenkill Railroad | D&H | 1902 | 1903 | Greenwich and Johnsonville Railway |
| Bennington and Rutland Railroad | RUT | 1865 | 1870 | Harlem Extension Railroad |
| Bennington and Rutland Railway | RUT | 1877 | 1901 | Rutland Railroad |
| Black River and Morristown Railroad | NYC | 1870 | 1883 | Utica and Black River Railroad |
| Black River and St. Lawrence Railway | NYC | 1868 | 1883 | Carthage and Adirondack Railway |
| Black River and Utica Railroad | NYC | 1853 | 1860 | Utica and Black River Railroad |
| Blossburg and Corning Railroad | NYC | 1854 | 1873 | Corning, Cowanesque and Antrim Railway |
| Bombay and Moira Railroad | 1898 | 1898 | N/A (operated by Ogdensburg and Lake Champlain Railroad) |
| Boston and Albany Railroad | B&A, BA | NYC | 1870 | 1961 | New York Central Railroad |
| Boston, Hartford and Erie Railroad | NH | 1864 | 1874 | New York and New England Railroad |
| Boston, Hartford and Erie Extension Railroad | NH | 1863 | 1864 | Boston, Hartford and Erie Railroad |
| Boston, Hartford and Erie Ferry Extension Railroad | NH | 1864 | 1864 | Boston, Hartford and Erie Railroad |
| Boston, Hoosac Tunnel and Western Railway | B&M | 1877 | 1892 | Fitchburg Railroad |
| Boston and Maine Corporation | BM | B&M | 1964 | Still exists as a lessor of Pan Am Railways operating subsidiary Springfield Terminal Railway |
| Boston and Maine Railroad | B&M, BM | B&M | 1900 | 1964 | Boston and Maine Corporation |
| Bradford, Eldred and Cuba Railroad | 1881 | 1893 | N/A |
| Bradford, Richburg and Cuba Railroad | 1881 | 1893 | N/A (operated by Bradford, Eldred and Cuba Railroad) |
| Brighton and Bensonhurst Railroad | 1892 | N/A | Never operated |
| Brooklyn, Bath and Coney Island Railroad | 1862 | 1885 | Brooklyn, Bath and West End Railroad |
| Brooklyn, Bath and West End Railroad | 1885 | 1898 | Atlantic Avenue Railroad | Electrified in 1893 |
| Brooklyn and Brighton Beach Railroad | 1887 | 1899 | Sea View Railroad |
| Brooklyn Central and Jamaica Railroad | LIRR | 1860 | 1865 | Brooklyn and Jamaica Railway |
| Brooklyn Eastern District Terminal | BEDT | 1906 | 1983 | New York Cross Harbor Railroad Terminal Corporation |
| Brooklyn, Flatbush and Coney Island Railway | 1877 | 1887 | Brooklyn and Brighton Beach Railroad |
| Brooklyn and Jamaica Railroad | LIRR | 1832 | 1860 | Brooklyn Central and Jamaica Railroad |
| Brooklyn and Jamaica Railway | LIRR | 1866 | 1872 | Atlantic Avenue Railroad |
| Brooklyn and Montauk Railroad | LI | 1879 | 1889 | Long Island Rail Road |
| Brooklyn and Rockaway Beach Railroad | 1863 | 1906 | Canarsie Railroad |
| Buffalo and Allegheny Valley Railroad | PRR | 1853 | 1865 | Buffalo and Washington Railway |
| Buffalo, Attica and Arcade Railroad | 1894 | 1917 | Arcade and Attica Railroad |
| Buffalo and Black Rock Railroad | NYC | 1833 | 1834 | Buffalo and Niagara Falls Railroad |
| Buffalo, Bradford and Pittsburgh Railroad | ERIE | 1859 | 1941 | Erie Railroad |
| Buffalo Branch of the Erie Railway | ERIE | 1861 | 1862 | Erie Railway |
| Buffalo, Chautauqua Lake and Pittsburgh Railway | PRR | 1879 | 1880 | Pittsburgh, Titusville and Buffalo Railway |
| Buffalo, Cleveland and Chicago Railway | NKP | 1881 | 1881 | New York, Chicago and St. Louis Railway |
| Buffalo and Cohocton Valley Railway | ERIE | 1850 | 1852 | Buffalo, Corning and New York Railroad |
| Buffalo, Corning and New York Railroad | ERIE | 1852 | 1857 | Buffalo, New York and Erie Railroad |
| Buffalo, Corry and Pittsburgh Railroad | PRR | 1867 | 1872 | Dunkirk, Chautauqua Lake and Pittsburgh Railroad |
| Buffalo Creek Railroad | BCK | ERIE/ LV | 1869 | 1983 | Consolidated Rail Corporation |
| Buffalo Creek Transfer Railroad | 1881 | 1914 | N/A |
| Buffalo and Erie Railroad | NYC | 1867 | 1869 | Lake Shore and Michigan Southern Railway |
| Buffalo Erie Basin Railroad | NYC | 1876 | 1913 | New York Central and Hudson River Railroad |
| Buffalo Extension of the Atlantic and Great Western Railway | ERIE | 1864 | 1865 | Atlantic and Great Western Railway |
| Buffalo and Geneva Railway | LV | 1889 | 1890 | Lehigh Valley Railway |
| Buffalo and Jamestown Railroad | ERIE | 1872 | 1877 | Buffalo and South Western Railroad |
| Buffalo and Lockport Railroad | NYC | 1852 | 1853 | New York Central Railroad |
| Buffalo and New York City Railroad | ERIE | 1851 | 1861 | Buffalo Branch of the Erie Railway, Buffalo, New York and Erie Railroad |
| Buffalo, New York and Erie Railroad | ERIE | 1857 | 1896 | Erie Railroad |
| Buffalo, New York and Philadelphia Railroad | PRR | 1883 | 1887 | Western New York and Pennsylvania Railway of New York |
| Buffalo, New York and Philadelphia Railway | PRR | 1871 | 1883 | Buffalo, New York and Philadelphia Railroad |
| Buffalo and Niagara Falls Railroad | NYC | 1834 | 1869 | New York Central Railroad |
| Buffalo and Oil Creek Cross Cut Railroad | PRR | 1865 | 1867 | Buffalo, Corry and Pittsburgh Railroad |
| Buffalo and Pittsburgh Railroad | ERIE | 1852 | 1859 | Buffalo, Bradford and Pittsburgh Railroad |
| Buffalo, Pittsburgh and Western Railroad | PRR | 1881 | 1883 | Buffalo, New York and Philadelphia Railroad |
| Buffalo, Pittsburgh and Western Railway | PRR | 1880 | 1881 | Buffalo, Pittsburgh and Western Railroad |
| Buffalo and Rochester Railroad | NYC | 1850 | 1853 | New York Central Railroad |
| Buffalo, Rochester and Pittsburgh Railroad | B&O | 1885 | 1887 | Buffalo, Rochester and Pittsburgh Railway |
| Buffalo, Rochester and Pittsburgh Railroad | B&O | 1881 | 1881 | Rochester and Pittsburgh Railroad |
| Buffalo, Rochester and Pittsburgh Railway | BR&P | B&O | 1887 | Still exists as a nonoperating subsidiary of CSX Transportation, leased to the Buffalo and Pittsburgh Railroad |
| Buffalo and South Western Railroad | ERIE | 1877 | 1895 | Erie Railroad |
| Buffalo and State Line Railroad | NYC | 1848 | 1867 | Buffalo and Erie Railroad |
| Buffalo and Susquehanna Railroad | B&O | 1954 | 1954 | Baltimore and Ohio Railroad |
| Buffalo and Susquehanna Railroad | B&S | B&O | 1910 | 1932 | Baltimore and Ohio Railroad |
| Buffalo and Susquehanna Railroad | B&O | 1896 | 1907 | Buffalo and Susquehanna Railway |
| Buffalo and Susquehanna Railway | 1902 | 1915 | Wellsville and Buffalo Railroad |
| Buffalo, Thousand Islands & Portland Railroad | NYC | 1850 | 1907 | Rome, Watertown and Ogdensburg Railroad |
| Buffalo and Washington Railroad | PRR | 1865 | 1865 | Buffalo and Washington Railway |
| Buffalo and Washington Railway | PRR | 1865 | 1871 | Buffalo, New York and Philadelphia Railway |
| Bush Terminal Railroad | 1903 |
| Cairo Railroad | 1884 | 1918 | N/A (operated by Catskill Mountain Railroad) |
| Campbell Hall Connecting Railroad | LNE | 1889 | 1961 | N/A |
| Canada Southern Railway | CASO | NYC | 1883 | 1904 | Michigan Central Railroad |
| Canajoharie and Catskill Railroad | 1830 | 1842 | Catskill Mountain Railroad |
| Canal Railroad | LV | 1878 | 1905 | Lehigh Valley Railway |
| Canandaigua and Corning Railroad | PRR | 1845 | 1852 | Canandaigua and Elmira Railroad |
| Canandaigua and Elmira Railroad | PRR | 1852 | 1857 | Elmira, Canandaigua and Niagara Falls Railroad |
| Canandaigua Lake Railroad | PRR | 1887 | 1888 | Elmira and Lake Ontario Railroad |
| Canandaigua and Niagara Falls Railroad | NYC | 1851 | 1857 | Niagara Bridge and Canandaigua Railroad |
| Canarsie Railroad | 1906 | 1912 | New York Consolidated Railroad | Electrified in 1906 |
| Canastota Northern Railroad | LV | 1886 | 1905 | Elmira, Cortland and Northern Railroad |
| Carthage and Adirondack Railway | NYC | 1883 | 1913 | New York Central and Hudson River Railroad |
| Carthage and Copenhagen Railroad | 1906 | 1917 | Deer River Railroad |
| Carthage, Watertown and Sackets Harbor Railroad | NYC | 1869 | 1913 | New York Central and Hudson River Railroad |
| Castleton and West Stockbridge Railroad | NYC | 1834 | 1836 | Albany and West Stockbridge Railroad |
| Catskill Mountain Railroad | 1917 | 1918 | N/A |
| Catskill Mountain Railroad | 1880 | 1885 | Catskill Mountain Railway |
| Catskill Mountain Railway | 1885 | 1916 | Catskill Mountain Railroad |
| Catskill and Tannersville Railway | 1892 | 1916 | Catskill Mountain Railroad |
| Cayuga Railway | LV | 1874 | 1877 | Cayuga Southern Railroad |
| Cayuga Lake Railroad | LV | 1867 | 1874 | Cayuga Railway |
| Cayuga Southern Railroad | LV | 1877 | 1879 | Geneva, Ithaca and Sayre Railroad |
| Cayuga and Susquehanna Railroad | DL&W | 1843 | 1946 | Delaware, Lackawanna and Western Railroad |
| Cazenovia and Canastota Railroad | LV | 1868 | 1873 | Cazenovia and Canastota Railway |
| Cazenovia and Canastota Railway | LV | 1873 | 1873 | Cazenovia, Canastota and De Ruyter Railroad |
| Cazenovia, Canastota and De Ruyter Railroad | LV | 1873 | 1876 | Cazenovia, Canastota and De Ruyter Railway |
| Cazenovia, Canastota and De Ruyter Railway | LV | 1876 | 1884 | Elmira, Cortland and Northern Railroad |
| Cazenovia and De Ruyter Railroad | LV | 1872 | 1873 | Cazenovia, Canastota and De Ruyter Railroad |
| Central Railroad Extension Company | LI | 1873 | 1882 | Long Island Rail Road |
| Central Railroad of Long Island | LI | 1871 | 1879 | Long Island Rail Road |
| Central New England Railway | CNE | NH | 1899 | 1927 | New York, New Haven and Hartford Railroad |
| Central New England and Western Railroad | NH | 1889 | 1892 | Philadelphia, Reading and New England Railroad |
| Central New York and Northern Railroad | PS&N | 1899 | 1899 | Central New York and Western Railroad |
| Central New York Southern Railroad | 1914 | 1923 | N/A |
| Central New York and Western Railroad | PS&N | 1892 | 1899 | Pittsburg, Shawmut and Northern Railroad |
| Central Valley Railroad | 1870 | 1875 | N/A |
| Central Vermont Railroad | CN | 1873 | 1899 | Central Vermont Railway |
| Central Vermont Railway | CV | CN | 1898 | 1962 | N/A |
| Champagne Railroad | CGNE | 1993 | 1996 | Livonia, Avon and Lakeville Railroad |
| Champlain and St. Lawrence Railroad | CN | 1851 | 1960 | Canadian National Railway |
| Chateaugay Railroad | D&H | 1879 | 1903 | Chateaugay and Lake Placid Railway |
| Chateaugay Railway | D&H | 1887 | 1903 | Chateaugay and Lake Placid Railway |
| Chateaugay and Lake Placid Railway | D&H | 1903 | 1957 | Delaware and Hudson Railroad |
| Chatham and Lebanon Valley Railroad | RUT | 1899 | 1901 | Rutland Railroad |
| Chautauqua Lake Railway | 1886 | 1894 | Jamestown and Lake Erie Railway |
| Chemung Railroad | PRR | 1845 | 1886 | Elmira and Lake Ontario Railroad |
| Cherry Valley and Mohawk River Railroad | D&H | 1864 | 1869 | Cherry Valley, Sharon and Albany Railroad |
| Cherry Valley, Sharon and Albany Railroad | D&H | 1869 | 1908 | Delaware and Hudson Company |
| Cherry Valley and Sprakers Railroad | D&H | 1860 | 1864 | Cherry Valley and Mohawk River Railroad |
| Chesapeake and Ohio Railway | C&O, CO | C&O | 1947 | 1987 | CSX Transportation |
| Clayton and Theresa Railroad | NYC | 1871 | 1886 | Utica and Black River Railroad |
| Clove Branch Railroad | 1868 | 1898 | N/A (operated by Newburgh, Dutchess and Connecticut Railroad) |
| Conesus Lake Railroad | ERIE | 1882 | 1932 | Erie Railroad |
| Coney Island and East River Railway | 1876 | 1877 | Brooklyn, Flatbush and Coney Island Railway |
| Conhocton Valley Railroad | 2001 | 2001 | B&H Rail Corporation |
| Connecting Terminal Railroad | PRR | 1881 | 1931 | Western New York and Pennsylvania Railway |
| Consolidated Rail Corporation | CR | 1976 | 1999 | CSX Transportation, Norfolk Southern Railway |
| Cooperstown and Charlotte Valley Railroad | D&H | 1888 | 1957 | Delaware and Hudson Railroad |
| Cooperstown and Charlotte Valley Railway | CACV | 1971 | 1989 | N/A |
| Cooperstown and Susquehanna Valley Railroad | D&H | 1865 | 1957 | Delaware and Hudson Railroad |
| Corning and Blossburg Railroad | NYC | 1851 | 1852 | Blossburg and Corning Railroad |
| Corning, Cowanesque and Antrim Railway | NYC | 1873 | 1892 | Fall Brook Railway |
| Cornwall Bridge Company | NYC | 1897 | 1917 | New York Central Railroad |
| Cranberry Lake Railroad | 1902 | 1914 | N/A |
| Danbury Terminal Railroad | DTRR | 1993 | 1996 | Housatonic Railroad |
| Dansville and Mount Morris Railroad | D&MM, DMM | 1891 | Still exists as a nonoperating subsidiary of the Rochester and Southern Railroad |
| Deer River Railroad | 1917 | 1918 | N/A |
| Degnon Terminal Railroad | LIRR | 1913 | 1928 | Long Island Rail Road |
| Delaware and Eastern Railroad | 1904 | 1911 | Delaware and Northern Railroad |
| Delaware and Eastern Railway | 1907 | 1911 | Delaware and Northern Railroad |
| Delaware and Hudson Company | D&H | 1899 | 1930 | Delaware and Hudson Railroad |
| Delaware and Hudson Railroad | D&H | D&H | 1930 | 1968 | Delaware and Hudson Railway |
| Delaware and Hudson Canal Company | D&H | 1867 | 1899 | Delaware and Hudson Company |
| Delaware, Lackawanna and Western Railroad | DL&W, DLW | DL&W | 1870 | 1960 | Erie–Lackawanna Railroad |
| Delaware and Northern Railroad | D&N | 1911 | 1928 | Delaware and Northern Railway |
| Delaware and Northern Railway | D&N | 1928 | 1942 | N/A |
| Delaware and Otsego Railroad | NYC | 1887 | 1901 | Ulster and Delaware Railroad |
| Depew and Tonawanda Railroad | LV | 1895 | 1903 | Lehigh Valley Railway |
| Dexter and Northern Railroad | 1908 | 1956 | N/A |
| Direct Railway between Syracuse and Rochester | NYC | 1848 | 1850 | Rochester and Syracuse Railroad |
| Dolgeville and Salisbury Railway | NYC | 1907 | 1917 | New York Central Railroad |
| Dunkirk, Allegheny Valley and Pittsburgh Railroad | NYC | 1873 | 1914 | New York Central Railroad |
| Dunkirk, Chautauqua Lake and Pittsburgh Railroad | PRR | 1879 | 1879 | Buffalo, Chautauqua Lake and Pittsburgh Railway |
| Dunkirk and State Line Railroad | NYC | 1850 | 1851 | Buffalo and State Line Railroad |
| Dunkirk, Warren and Pittsburgh Railroad | NYC | 1867 | 1870 | Dunkirk, Warren and Pittsburgh Railway |
| Dunkirk, Warren and Pittsburgh Railway | NYC | 1870 | 1873 | Dunkirk, Allegheny Valley and Pittsburgh Railroad |
| Dutchess and Columbia Railroad | NH | 1866 | 1872 | New York, Boston and Northern Railway |
| Dutchess County Railroad | NH | 1890 | 1907 | Central New England Railway |
| East River Terminal Railroad | 1907 | 1916 | Brooklyn Eastern District Terminal |
| Ellenville and Kingston Railroad | NH | 1901 | 1957 | N/A |
| Elmira, Canandaigua and Niagara Falls Railroad | PRR | 1857 | 1858 | Elmira, Jefferson and Canandaigua Railroad |
| Elmira, Cortland and Northern Railroad | LV | 1884 | 1905 | Lehigh Valley Railway |
| Elmira, Jefferson and Canandaigua Railroad | PRR | 1859 | 1886 | Elmira and Lake Ontario Railroad |
| Elmira and Lake Ontario Railroad | PRR | 1886 | 1956 | Northern Central Railway |
| Elmira State Line Railroad | ERIE | 1872 | 1942 | N/A |
| Elmira and Williamsport Railroad | PRR | 1860 | 1969 | Penndel Company |
| Erie Railroad | ERIE | ERIE | 1895 | 1960 | Erie–Lackawanna Railroad |
| Erie Railway | ERIE | 1861 | 1878 | New York, Lake Erie and Western Railroad |
| Erie and Black Rock Railroad | ERIE | 1882 | 1932 | Erie Railroad |
| Erie and Central New York Railroad | DL&W | 1902 | 1945 | Delaware, Lackawanna and Western Railroad |
| Erie and Central New York Railway | DL&W | 1863 | 1902 | Erie and Central New York Railroad |
| Erie and Genesee Valley Railroad | ERIE | 1868 | 1891 | Dansville and Mount Morris Railroad |
| Erie International Railway | ERIE | 1872 | 1895 | Erie Railroad |
| Erie and Jersey Railroad | ERIE | 1905 | 1915 | Erie Railroad |
| Erie–Lackawanna Railroad | EL | 1960 | 1968 | Erie Lackawanna Railway |
| Erie Lackawanna Railway | EL | 1968 | 1976 | Consolidated Rail Corporation |
| Erie and New York City Railroad | ERIE | 1851 | 1860 | Atlantic and Great Western Railroad |
| Erie Terminals Railroad | ERIE | 1907 | 1915 | Erie Railroad |
| Fall Brook Railway | NYC | 1892 | 1909 | Geneva, Corning and Southern Railroad |
| Far Rockaway Branch Railroad | LI | 1868 | 1872 | South Side Railroad of Long Island |
| Fitchburg Railroad | B&M | 1887 | 1919 | Boston and Maine Railroad |
| Flatbush and Coney Island Park and Concourse Railroad | 1876 | 1877 | Brooklyn, Flatbush and Coney Island Railway |
| Flushing Railroad | LI | 1852 | 1859 | New York and Flushing Railroad |
| Flushing and North Side Railroad | LI | 1868 | 1881 | Long Island City and Flushing Railroad |
| Flushing and Woodside Railroad | LI | 1864 | 1871 | Flushing and North Side Railroad |
| Fonda, Johnstown and Gloversville Railroad | FJG | 1867 | 1984 | N/A |
| Friendship Railroad | PS&N | 1880 | 1881 | Allegany Central Railroad |
| Fulton Chain Railroad | NYC | 1896 | 1902 | Fulton Chain Railway |
| Fulton Chain Railway | NYC | 1902 | 1937 | New York Central Railroad |
| Fulton and Oswego Railroad | NYC | 1885 | 1886 | Syracuse, Phoenix and Oswego Railway |
| Garnerville Railroad | ERIE | 1875 | | N/A |
| Genesee Falls Railway | NYC | 1886 |
| Genesee River Railroad | ERIE | 1905 | 1915 | Erie Railroad |
| Genesee Valley Canal Railroad | PRR | 1880 | 1912 | Pennsylvania and Rochester Railroad |
| Genesee Valley Terminal Railroad | PRR | 1882 | 1912 | Pennsylvania and Rochester Railroad |
| Genesee and Wyoming Railroad | GNW, GNWR | 1899 | Still exists as a nonoperating subsidiary of the Rochester and Southern Railroad |
| Genesee and Wyoming Valley Railway | 1891 | 1899 | Genesee and Wyoming Railroad |
| Geneseo Valley Railroad | ERIE | 1857 | 1860 | Avon, Geneseo and Mount Morris Railroad |
| Geneva, Corning and Southern Railroad | NYC | 1909 | 1914 | New York Central Railroad |
| Geneva, Corning and Southern Railway | NYC | 1875 | 1909 | Geneva, Corning and Southern Railroad |
| Geneva and Hornellsville Railway | PRR | 1875 | 1876 | Geneva, Hornellsville and Pine Creek Railway |
| Geneva, Hornellsville and Pine Creek Railway | PRR | 1876 | 1879 | Lake Ontario Southern Railway |
| Geneva and Ithaca Railroad | LV | 1870 | 1874 | Geneva, Ithaca and Athens Railroad |
| Geneva, Ithaca and Athens Railroad | LV | 1874 | 1876 | Geneva, Ithaca and Sayre Railroad |
| Geneva, Ithaca and Sayre Railroad | LV | 1876 | 1889 | Geneva and Sayre Railroad |
| Geneva and Lyons Railroad | NYC | 1877 | 1890 | New York Central and Hudson River Railroad |
| Geneva and Sayre Railroad | LV | 1889 | 1890 | Geneva and Van Ettenville Railway |
| Geneva and Southwestern Railway | PRR | 1871 | 1875 | Geneva and Hornellsville Railway |
| Geneva Southwestern and Hornellsville Railway | PRR | 1872 | 1875 | Geneva and Hornellsville Railway |
| Geneva and Van Ettenville Railway | LV | 1889 | 1890 | Lehigh Valley Railway |
| Glen Cove Branch Rail Road | LI | 1865 | | Long Island Rail Road |
| Glendale and East River Railroad | LI | 1874 | 1928 | Long Island Rail Road |
| Glenfield and Western Railroad | 1901 | | N/A |
| Glens Falls Railroad | D&H | 1867 | 1906 | Rensselaer and Saratoga Railroad |
| Gloversville and Broadalbin Railroad | 1895 | 1931 | Fonda, Johnstown and Gloversville Railroad |
| Gloversville and Northville Railroad | 1872 | 1881 | Fonda, Johnstown and Gloversville Railroad |
| Goshen and Deckertown Railway | ERIE | 1868 | 1954 | Erie Railroad |
| Gouverneur and Oswegatchie Railroad | NYC | 1892 | 1913 | New York Central and Hudson River Railroad |
| Grand Trunk Railway | GT | CN | 1864 | 1923 | Canadian National Railway |
| Grasse River Railroad | GR | 1915 | 1959 | N/A |
| Great Neck and Port Washington Railroad | LI | 1896 | 1902 | Long Island Rail Road |
| Great Valley and Bradford Railroad | B&O | 1881 | 1881 | Rochester and Pittsburgh Railroad |
| Great Western Railway | CN | 1855 | 1882 | Grand Trunk Railway |
| Greigsville and Pearl Creek Railroad | 1897 | 1899 | N/A |
| Greene Railroad | DL&W | 1869 | 1946 | Delaware, Lackawanna and Western Railroad |
| Greenwich and Johnsonville Railroad | D&H | 1874 | 1879 | Greenwich and Johnsonville Railway |
| Greenwich and Johnsonville Railway | G&J, GJ | D&H | 1879 | 1982 | Batten Kill Railroad |
| Greenwood and Coney Island Railroad | 1872 | 1874 | Prospect Park and Coney Island Railroad |
| Hackensack and New York Extension Railroad | ERIE | 1869 | 1873 | New Jersey and New York Railway |
| Halite and Northern Railroad | 1910 | 1933 | N/A (operated by Genesee and Wyoming Railroad) |
| Hancock and East Branch Railroad | 1906 | 1907 | Delaware and Eastern Railway |
| Hancock and Pennsylvania Railroad | NH | 1889 | 1889 | Ontario, Carbondale and Scranton Railway |
| Harlem Extension Railroad | RUT | 1870 | 1873 | New York, Boston and Montreal Railway |
| Harlem Extension Railroad South Coal Transportation Company | RUT | 1877 | 1880 | N/A | Leased the New York, Boston and Montreal Railway |
| Harlem River and Port Chester Railroad | NH | 1866 | 1927 | New York, New Haven and Hartford Railroad |
| Hartford and Connecticut Western Railroad | NH | 1882 | 1947 | New York, New Haven and Hartford Railroad |
| Hayts Corners, Ovid and Willard Railroad | LV | 1882 | 1959 | N/A |
| Hempstead and Rockaway Railroad | LIRR | 1869 | 1871 | New York and Hempstead Railroad |
| Herkimer, Newport and Poland Railway | NYC | 1891 | 1892 | Mohawk and Malone Railway |
| Herkimer, Newport and Poland Extension Railway | NYC | 1891 | 1892 | Mohawk and Malone Railway |
| Herkimer, Newport and Poland Narrow Gauge Railway | NYC | 1880 | 1891 | Herkimer, Newport and Poland Railway |
| Hicksville and Cold Spring Branch Railroad | LI | 1853 | 1870 | Long Island Rail Road |
| Hobart Branch Railroad | NYC | 1884 | 1901 | Ulster and Delaware Railroad |
| Hoosac Tunnel and Saratoga Railway | B&M | 1881 | 1886 | Troy, Saratoga and Northern Railroad |
| Hudson and Berkshire Railroad | NYC | 1832 | 1854 | Hudson and Boston Railroad |
| Hudson and Boston Railroad | NYC | 1855 | 1870 | Boston and Albany Railroad |
| Hudson Connecting Railroad | NH | 1887 | 1889 | Central New England and Western Railroad |
| Hudson Light and Power and Railroad Company | 1899 | 1899 | Albany and Hudson Railway and Power Company |
| Hudson River Railroad | NYC | 1846 | 1869 | New York Central and Hudson River Railroad |
| Hudson River Bridge Company at Albany | NYC | 1856 | 1976 | Consolidated Rail Corporation |
| Hudson River Connecting Railroad | NYC | 1913 | 1964 | New York Central Railroad |
| Hudson River West Shore Railroad | NYC | 1867 | 1868 | West Shore Hudson River Railroad |
| Hunter's Point and South Side Railroad | LI | 1870 | 1872 | South Side Railroad of Long Island |
| International Bridge Company | CN | 1857 | 1956 | Canadian National Railway |
| Island Railroad | 1883 |
| Ithaca and Athens Railroad | LV | 1870 | 1874 | Geneva, Ithaca and Athens Railroad |
| Ithaca, Auburn and Western Railroad | LV | 1876 | 1890 | Auburn and Ithaca Railway |
| Ithaca and Cortland Railroad | LV | 1869 | 1871 | Utica, Ithaca and Elmira Railroad |
| Ithaca and Owego Railroad | DL&W | 1828 | 1843 | Cayuga and Susquehanna Railroad |
| Ithaca and Tonawanda Railroad | LV | 1865 | 1870 | Ithaca and Athens Railroad |
| Jamaica and South Shore Railroad | LI | 1903 | 1912 | Long Island Rail Road |
| Jamestown and Chautauqua Railway | 1898 | 1913 | Jamestown, Westfield and Northwestern Railroad |
| Jamestown, Chautauqua and Lake Erie Railway | 1900 | 1913 | Jamestown, Westfield and Northwestern Railroad |
| Jamestown and Lake Erie Railway | 1894 | 1898 | Jamestown and Chautauqua Railway |
| Jamestown, Westfield and Northwestern Railroad | 1913 | 1950 | N/A | Electric from 1914 to 1947 |
| Jay Street Connecting Railroad | 1909 |
| Jay Street Extension Railroad | 1916 | 1916 | Jay Street Connecting Railroad |
| Jersey City and Albany Railroad | NYC | 1873 | 1877 | Jersey City and Albany Railway |
| Jersey City and Albany Railway | NYC | 1878 | 1881 | North River Railroad |
| Junction Railroad | NYC | 1870 | 1879 | New York Central and Hudson River Railroad |
| Kaaterskill Railroad | NYC | 1882 | 1901 | Ulster and Delaware Railroad |
| Kanona and Prattsburg Railroad | 1886 | 1893 | Kanona and Prattsburg Railway |
| Kanona and Prattsburg Railway | 1897 | 1917 | Prattsburg Railway |
| Keeseville, Ausable Chasm and Lake Champlain Railroad | 1889 | 1924 | N/A | Electric from 1905 to 1911 |
| Kinderhook and Hudson Railway | 1889 | 1899 | Hudson Light and Power and Railroad Company |
| Kings County Central Railroad | 1876 | 1878 | N/A |
| Lackawanna and Pittsburgh Railroad | PS&N | 1882 | 1889 | Lackawanna and Southwestern Railroad |
| Lackawanna and Southwestern Railroad | PS&N | 1889 | 1892 | Central New York and Western Railroad |
| Lackawanna and Susquehanna Railroad | D&H | 1867 | |
| Lake Champlain and Moriah Railroad | 1867 | 1968 | N/A |
| Lake Ontario Railroad | NYC | 1874 | 1875 | Rome, Watertown and Ogdensburg Railroad |
| Lake Ontario and Hudson River Railroad | D&H | 1857 | 1860 | Adirondac Estate and Railroad Company |
| Lake Ontario Shore Railroad | NYC | 1868 | 1874 | Lake Ontario Railroad |
| Lake Ontario Southern Railway | PRR | 1879 | 1882 | Sodus Bay and Southern Railroad |
| Lake Shore and Michigan Southern Railway | NYC | 1869 | 1914 | New York Central Railroad |
| Lebanon Springs Railroad | RUT | 1893 | 1899 | Chatham and Lebanon Valley Railroad |
| Lebanon Springs Railroad | RUT | 1852 | 1870 | Harlem Extension Railroad |
| Lehigh – Buffalo Terminal Railway | LV | 1915 | |
| Lehigh and Hudson River Railway | L&HR, LHR | L&HR | 1882 | 1976 | Consolidated Rail Corporation |
| Lehigh and Lake Erie Railroad | LV | 1896 | 1907 | Lehigh Valley Railway |
| Lehigh and New England Railroad | LNE | LNE | 1895 | 1961 | N/A |
| Lehigh and New York Railroad | LV | 1895 | 1949 | Lehigh Valley Railroad |
| Lehigh Valley Railroad | LV | LV | 1888 | 1976 | Consolidated Rail Corporation |
| Lehigh Valley Railway | LV | 1882 | 1949 | Lehigh Valley Railroad |
| Lewiston Railroad | NYC | 1836 | 1855 | New York Central Railroad |
| Lincoln Park and Charlotte Railroad | B&O | 1888 | 1899 | Buffalo, Rochester and Pittsburgh Railway |
| Little Falls and Dolgeville Railroad | NYC | 1891 | 1913 | New York Central and Hudson River Railroad |
| Lockport and Buffalo Railway | ERIE | 1871 | 1895 | Erie Railroad |
| Lockport and Niagara Falls Railroad | NYC | 1834 | 1850 | Rochester, Lockport and Niagara Falls Railroad |
| Long Island Rail Road | LI | LI | 1834 | 1997 | New York and Atlantic Railway | Still exists as a passenger railroad |
| Long Island Railroad North Shore Branch | LI | 1892 | 1921 | Long Island Rail Road |
| Long Island City and Flushing Railroad | LI | 1881 | 1889 | Long Island Rail Road |
| Long Island City and Manhattan Beach Railroad | LI | 1883 | 1885 | New York, Brooklyn and Manhattan Beach Railway |
| Mahopac Falls Railroad | NYC | 1884 | 1913 | New York and Putnam Railroad |
| Malone and St. Lawrence Railway | NYC | 1891 | 1895 | St. Lawrence and Adirondack Railway |
| Marcellus Electric Railroad | 1887 | 1905 | Marcellus and Otisco Lake Railway |
| Marcellus and Otisco Company | 1919 | 1959 | N/A |
| Marcellus and Otisco Lake Railway | 1905 | 1920 | Marcellus and Otisco Company |
| Marion Railway | PRR | 1917 | 1931 | Elmira and Lake Ontario Railroad |
| Massena Springs and Fort Covington Railroad | CN | 1884 | 1888 | United States and Canada Railroad |
| Mayville Extension Railroad | 1881 | 1887 | Chautauqua Lake Railway |
| Mechanicville and Fort Edward Railroad | B&M | 1880 | |
| Michigan Central Railroad | MC | NYC | 1904 | 1930 | New York Central Railroad |
| Middleburgh and Schoharie Railroad | 1867 | 1936 | N/A |
| Middlesex Valley Railroad | LV | 1892 | 1903 | Lehigh Valley Railway |
| Middletown and Crawford Railroad | ERIE | 1868 | 1932 | Erie Railroad |
| Middletown and New Jersey Railway | MNJ | 1947 | 2009 | Middletown and New Jersey Railroad |
| Middletown and Unionville Railroad | M&U, MU | 1913 | 1947 | Middletown and New Jersey Railway |
| Middletown, Unionville and Water Gap Railroad | ERIE | 1866 | 1913 | Middletown and Unionville Railroad |
| Midland Railroad of New Jersey | ERIE | 1880 | 1881 | New York, Susquehanna and Western Railroad |
| Mohawk and Adirondack Railroad | NYC | 1891 | 1891 | Herkimer, Newport and Poland Extension Railway, St. Lawrence and Adirondack Railroad |
| Mohawk and Hudson Railroad | NYC | 1826 | 1847 | Albany and Schenectady Railroad |
| Mohawk and Malone Railway | NYC | 1892 | 1913 | New York Central and Hudson River Railroad |
| Mohawk Valley Railroad | NYC | 1851 | 1853 | New York Central Railroad |
| Mohawk Valley and Northern Railway | NYC | 1890 | 1891 | Herkimer, Newport and Poland Narrow Gauge Railway |
| Montauk Extension Railroad | LI | 1893 | 1902 | Long Island Rail Road |
| Montclair Railway | ERIE | 1867 | 1875 | Montclair and Greenwood Lake Railway |
| Montclair and Greenwood Lake Railway | ERIE | 1875 | 1878 | New York and Greenwood Lake Railway |
| Montgomery and Erie Railway | ERIE | 1866 | 1954 | Erie Railroad |
| Monticello and Port Jervis Railway | NH | 1869 | 1875 | Port Jervis and Monticello Railroad |
| Montreal and Champlain Railroad | CN | 1857 | 1864 | Grand Trunk Railway |
| Montreal and Plattsburgh Railroad | D&H | 1868 | 1873 | New York and Canada Railroad |
| Mount McGregor Railroad | 1889 | 1898 | Saratoga Northern Railway |
| Nanuet and New City Railroad | ERIE | 1871 | | New Jersey and New York Railroad |
| Napierville Junction Railway | NJ | D&H | | Still exists as a nonoperating subsidiary of the Canadian Pacific Railway |
| New England Railroad | NH | 1895 | 1908 | New York, New Haven and Hartford Railroad |
| New Jersey Midland Railway | ERIE | 1874 | 1880 | Midland Railroad of New Jersey |
| New Jersey and New York Railroad | ERIE | 1880 | 1967 | Erie–Lackawanna Railroad |
| New Jersey and New York Railway | ERIE | 1873 | 1880 | New Jersey and New York Railroad |
| New Jersey and New York Extension Railroad | ERIE | 1886 | 1936 | New Jersey and New York Railroad |
| New York and Albany Railroad | NYC | 1832 | 1846 | New York and Harlem Railroad |
| New York and Atlantic Railway | 1880 | 1887 | West Brooklyn Railroad |
| New York, Auburn and Lansing Railroad | 1900 | 1914 | Central New York Southern Railroad |
| New York Bay Extension Railroad | LI | 1892 | 1902 | Long Island Rail Road |
| New York, Bay Ridge and Jamaica Railroad | LI | 1875 | 1885 | New York, Brooklyn and Manhattan Beach Railway |
| New York and Boston Railroad | NYC | 1869 | 1872 | New York, Boston and Northern Railway |
| New York, Boston and Montreal Railway | NH, NYC, RUT | 1873 | 1876 | Bennington and Rutland Railway, New York, Rutland and Montreal Railroad, New York, Westchester and Putnam Railway, Newburgh, Dutchess and Connecticut Railroad |
| New York, Boston and Northern Railway | NH, NYC | 1872 | 1873 | New York, Boston and Montreal Railway |
| New York and Brighton Beach Railway | 1878 | 1884 | Sea Beach and Brighton Railroad |
| New York, Brooklyn and Manhattan Beach Railway | LI | 1885 | 1925 | Long Island Rail Road |
| New York and Canada Railroad | D&H | 1872 | 1908 | Delaware and Hudson Company |
| New York Central Railroad | NYC | NYC | 1914 | 1968 | Penn Central Transportation Company |
| New York Central Railroad | NYC | 1853 | 1869 | New York Central and Hudson River Railroad |
| New York Central and Hudson River Railroad | NYC | 1869 | 1914 | New York Central Railroad |
| New York Central Niagara River Railroad | NYC | 1877 | 1913 | New York Central and Hudson River Railroad |
| New York, Chicago and St. Louis Railroad | NKP | NKP | 1887 | 1964 | Norfolk and Western Railway |
| New York, Chicago and St. Louis Railway | NKP | 1881 | 1887 | New York, Chicago and St. Louis Railroad |
| New York City and Northern Railroad | NYC | 1878 | 1887 | New York and Northern Railway |
| New York and Coney Island Railroad | 1879 | | South Brooklyn Railway | Electrified in 1899 |
| New York Connecting Railroad | NYCN | NH/ PRR | 1892 | 1976 | Consolidated Rail Corporation |
| New York Cross Harbor Railroad Terminal Corporation | NYCH | 1983 | 2006 | New York New Jersey Rail, LLC |
| New York Dock Railway | NYD | 1910 | 1983 | New York Cross Harbor Railroad Terminal Corporation |
| New York and Eastern Railway | NYER | 2003 | 2004 | N/A | Never operated |
| New York and Erie Railroad | ERIE | 1832 | 1861 | Erie Railway |
| New York and Flushing Railroad | LI | 1859 | 1891 | Long Island Rail Road |
| New York and Greenwood Lake Railway | ERIE | 1878 | 1943 | Erie Railroad |
| New York and Harlem Railroad | NYC | 1831 | Still exists as a lessor of the Metro-North Commuter Railroad |
| New York and Hempstead Railroad | LIRR | 1871 | 1875 | Southern Hempstead Branch Railroad |
| New York and Hempstead Plains Railroad | LIRR | 1870 | 1871 | New York and Hempstead Railroad |
| New York, Housatonic and Northern Railroad | 1863 | 1881 | Westchester Railway |
| New York and Jamaica Railroad | LI | 1859 | 1860 | Long Island Rail Road |
| New York, Kingston and Syracuse Railroad | NYC | 1872 | 1875 | Ulster and Delaware Railroad |
| New York, Lackawanna and Western Railway | DL&W | 1880 | 1945 | Delaware, Lackawanna and Western Railroad |
| New York, Lake Erie and Western Railroad | ERIE | 1878 | 1895 | Erie Railroad |
| New York and Long Beach Railroad | LI | 1880 | 1907 | Long Island Rail Road |
| New York and Mahopac Railroad | NYC | 1871 | 1880 | New York and Harlem Railroad |
| New York and Manhattan Beach Railway | LI | 1876 | 1885 | New York, Brooklyn and Manhattan Beach Railway |
| New York and Massachusetts Railway | NH | 1887 | 1893 | Poughkeepsie and Eastern Railway |
| New York and New England Railroad | NH | 1873 | 1895 | New England Railroad |
| New York and New Haven Railroad | NH | 1846 | 1872 | New York, New Haven and Hartford Railroad |
| New York, New Haven and Hartford Railroad | NH | NH | 1872 | 1969 | Penn Central Transportation Company |
| New York and Northern Railway | NYC | 1887 | 1893 | New York and Putnam Railroad |
| New York, Ontario and Western Railway | O&W, OW | NH | 1880 | 1957 | N/A |
| New York and Oswego Midland Railroad | NH | 1866 | 1879 | Ithaca, Auburn and Western Railroad, New York, Ontario and Western Railway |
| New York and Ottawa Railroad | NYC | 1897 | 1904 | New York and Ottawa Railway |
| New York and Ottawa Railway | NYC | 1905 | 1913 | New York Central and Hudson River Railroad |
| New York, Pennsylvania and Ohio Railroad | ERIE | 1880 | 1896 | Nypano Railroad |
| New York and Pennsylvania Railroad | 1896 | 1902 | New York and Pennsylvania Railway |
| New York and Pennsylvania Railway | 1904 | 1935 | N/A |
| New York and Putnam Railroad | NYC | 1894 | 1913 | New York Central and Hudson River Railroad |
| New York and Rockaway Railroad | LI | 1870 | 1903 | Jamaica and South Shore Railroad |
| New York and Rockaway Beach Railway | LI | 1887 | 1921 | Long Island Rail Road |
| New York, Rutland and Montreal Railroad | RUT | 1883 | 1893 | Lebanon Springs Railroad |
| New York and Sea Beach Railway | 1876 | 1896 | Sea Beach Railway |
| New York, Susquehanna and Western Railroad | ERIE | 1881 | 1958 | N/A |
| New York, West Shore and Buffalo Railway | NYC | 1880 | 1885 | West Shore Railroad |
| New York, West Shore and Chicago Railroad | NYC | 1870 | 1879 | New York, West Shore and Buffalo Railway |
| New York, Westchester and Putnam Railway | NYC | 1877 | 1878 | New York City and Northern Railroad |
| New York, Woodhaven and Rockaway Railroad | LI | 1877 | 1887 | New York and Rockaway Beach Railway |
| Newark and Marion Railway | PRR | 1900 | 1917 | Marion Railway |
| Newburgh, Dutchess and Connecticut Railroad | NH | 1877 | 1907 | Central New England Railway |
| Newburgh and New York Railway | ERIE | 1865 | 1895 | New York, Lake Erie and Western Railroad |
| Newton Falls and Northern Railroad | 1908 | 1919 | N/A |
| Newtown and Flushing Railroad | LIRR | 1871 | 1876 | N/A |
| Niagara Bridge and Canandaigua Railroad | NYC | 1858 | 1890 | New York Central and Hudson River Railroad |
| Niagara Falls Branch Railroad | NYC | 1875 | 1913 | New York Central and Hudson River Railroad |
| Niagara Falls International Bridge Company | CN | 1846 | |
| Niagara Junction Railway | NJ, NIAJ | ERIE/ LV/ NYC | 1892 | 1976 | Consolidated Rail Corporation | Electrified in 1913 |
| Niagara River Bridge Company | NYC | 1881 | 2002 | N/A | Still exists as an abandoned subsidiary of CNCP Niagara–Windsor Partnership, a nonoperating joint subsidiary of the Canadian National Railway and Canadian Pacific Railway |
| Nickel Plate Connecting Railroad | NKP | 1917 | |
| Norfolk and Western Railway | N&W, NW | 1964 | 1998 | Norfolk Southern Railway |
| North River Railroad | NYC | 1881 | 1881 | New York, West Shore and Buffalo Railway |
| North River Railway | NYC | 1880 | 1881 | North River Railroad |
| North Shore Railroad | LI | 1863 | 1884 | Long Island City and Flushing Railroad |
| Northern Railroad | RUT | 1845 | 1865 | Ogdensburg and Lake Champlain Railroad |
| Northern Railroad of New Jersey | ERIE | 1858 | 1943 | Erie Railroad |
| Northern Adirondack Railroad | NYC | 1883 | 1895 | Northern New York Railroad |
| Northern Adirondack Extension Railroad | NYC | 1886 | 1890 | Northern Adirondack Railroad |
| Northern Central Railway | PRR | 1956 | 1976 | Consolidated Rail Corporation |
| Northern Central Railway | PRR | 1863 | 1911 | Pennsylvania Railroad |
| Northern Extension of the Rochester, Nunda and Pennsylvania Railroad | PRR | 1872 | 1872 | Rochester, Nunda and Pennsylvania Railroad |
| Northern New York Railroad | NYC | 1895 | 1897 | New York and Ottawa Railroad |
| Norwood and Montreal Railroad | NYC | 1884 | 1889 | Rome, Watertown and Ogdensburg Railroad |
| Norwood and St. Lawrence Railroad | NSL | 1901 | 1974 | Ogdensburg and Norwood Railway |
| Nyack and Northern Railroad | ERIE | 1868 | 1892 | Nyack and Southern Railroad |
| Nyack and Southern Railroad | ERIE | 1899 | 1944 | Erie Railroad |
| Nypano Railroad | ERIE | 1896 | 1941 | Erie Railroad |
| Ogdensburg and Lake Champlain Railroad | RUT | 1864 | 1898 | Ogdensburg and Lake Champlain Railway |
| Ogdensburg and Lake Champlain Railway | RUT | 1898 | 1899 | Rutland Railroad |
| Ogdensburg and Morristown Railroad | NYC | 1871 | 1886 | Utica and Black River Railroad |
| Ogdensburg and Norwood Railway | ONRY | 1965 | 1977 | St. Lawrence Railroad |
| Olean Railroad | PS&N | 1880 | 1881 | Allegany Central Railroad |
| Olean, Bradford and Warren Railroad | PRR | 1877 | 1916 | Western New York and Pennsylvania Railway |
| Olean and Salamanca Railroad | PRR | 1882 | 1883 | Buffalo, New York and Philadelphia Railroad |
| Ontario, Carbondale and Scranton Railway | NH | 1889 | 1957 | N/A |
| Ontario Southern Railroad | PRR | 1875 | 1879 | Lake Ontario Southern Railway |
| Orange County Railroad | L&HR | 1888 | 1907 | Lehigh and Hudson River Railway |
| Oswego Railroad Bridge Company | NYC | 1872 | 1885 | Rome, Watertown and Ogdensburg Railroad |
| Oswego and Rome Railroad | NYC | 1863 | 1913 | New York Central and Hudson River Railroad |
| Oswego and Syracuse Railroad | DL&W | 1839 | 1945 | Delaware, Lackawanna and Western Railroad |
| Otis Railway | 1899 | 1916 | Catskill Mountain Railroad |
| Otis Elevating Railway | 1885 | 1899 | Otis Railway |
| Owasco River Railway | OR | LV/ NYC | 1881 | 1976 | N/A |
| Oyster Bay Extension Railroad | LI | 1886 | 1913 | Long Island Rail Road |
| Pecksport Connecting Railway | NH | 1886 | 1957 | N/A |
| Penn Central Transportation Company | PC | 1968 | 1976 | Consolidated Rail Corporation |
| Penn Yan and New York Railway | NYC | 1877 | 1885 | Syracuse, Geneva and Corning Railway |
| Penndel Company | PRR | 1955 | 1976 | Consolidated Rail Corporation |
| Pennsylvania Railroad | PRR | PRR | 1900 | 1968 | Penn Central Transportation Company |
| Pennsylvania, New York and Long Island Railroad | PRR | 1902 | 1907 | Pennsylvania Tunnel and Terminal Railroad |
| Pennsylvania and New York Canal and Railroad Company | LV | 1867 | 1888 | Lehigh Valley Railroad |
| Pennsylvania, Poughkeepsie and Boston Railroad | LNE | 1887 | 1895 | Lehigh and New England Railroad |
| Pennsylvania and Rochester Railroad | PRR | 1912 | 1916 | Western New York and Pennsylvania Railway |
| Pennsylvania Tunnel and Terminal Railroad | PRR | 1907 | 1976 | Consolidated Rail Corporation |
| Pere Marquette Railroad | C&O | 1904 | 1917 | Pere Marquette Railway |
| Pere Marquette Railway | PM | C&O | 1917 | 1947 | Chesapeake and Ohio Railway |
| Perry Railroad | B&O | 1882 | 1899 | Buffalo, Rochester and Pittsburgh Railway |
| Philadelphia, Reading and New England Railroad | NH | 1892 | 1899 | Central New England Railway |
| Pine Plains and Albany Railroad | RUT | 1872 | 1872 | Harlem Extension Railroad |
| Pittsburgh and New York Railroad | B&O | 1881 | 1881 | Rochester and Pittsburgh Railroad |
| Pittsburg, Shawmut and Northern Railroad | PS&N | 1899 | 1947 | N/A |
| Pittsburgh, Titusville and Buffalo Railway | PRR | 1880 | 1881 | Buffalo, Pittsburgh and Western Railroad |
| Plattsburgh and Dannemora Railroad | D&H | 1878 | |
| Plattsburgh and Montreal Railroad | D&H | 1850 | 1868 | Montreal and Plattsburgh Railroad |
| Pochuck Railroad | LNE | 1897 | 1944 | N/A |
| Port Chester Terminal Railroad | 1901 | |
| Port Dickinson and Chenango River Railroad | DL&W | 1881 | | N/A |
| Port Jervis and Monticello Railroad | NH | 1875 | 1886 | Port Jervis, Monticello and New York Railroad |
| Port Jervis, Monticello and New York Railroad | NH | 1886 | 1902 | Port Jervis, Monticello and Summitville Railroad |
| Port Jervis, Monticello and Summitville Railroad | NH | 1902 | 1957 | N/A |
| Potsdam and Watertown Railroad | NYC | 1852 | 1860 | Watertown and Rome Railroad |
| Poughkeepsie Bridge Company | NH | 1871 | 1892 | Poughkeepsie Bridge and Railroad Company |
| Poughkeepsie Bridge Railroad | NH | 1888 | 1907 | Central New England Railway |
| Poughkeepsie Bridge and Railroad Company | NH | 1892 | 1892 | Philadelphia, Reading and New England Railroad |
| Poughkeepsie and Connecticut Railroad | NH | 1888 | 1889 | Central New England and Western Railroad |
| Poughkeepsie and Eastern Railroad | NH | 1866 | 1875 | Poughkeepsie, Hartford and Boston Railroad |
| Poughkeepsie and Eastern Railway | NH | 1893 | 1907 | Central New England Railway |
| Poughkeepsie, Hartford and Boston Railroad | NH | 1875 | 1887 | Hartford and Connecticut Western Railroad, New York and Massachusetts Railway |
| Prattsburg Railway | 1917 | 1962 | N/A |
| Prospect Park and Coney Island Railroad | 1874 | | Electrified in 1899 |
| Prospect Park and South Brooklyn Railroad | 1888 | | Electrified in 1899 |
| Putnam and Dutchess Railroad | 1871 | 1872 | New York, Boston and Northern Railway |
| Raquette Lake Railway | NYC | 1899 | 1933 | N/A |
| Raymondville and Waddington Railroad | 1907 | 1908 | Norwood and St. Lawrence Railroad |
| Rensselaer and Saratoga Railroad | D&H | 1832 | 1945 | Delaware and Hudson Railroad |
| Rhinebeck and Connecticut Railroad | NH | 1870 | 1882 | Hartford and Connecticut Western Railroad |
| R.J. Corman Railroad/Allentown Lines | RJCN | 1996 | 2002 | N/A |
| Rochester and Charlotte Railroad | B&O | 1881 | 1881 | Rochester and Pittsburgh Railroad |
| Rochester and Genesee Valley Railroad | ERIE | 1851 | 1976 | Consolidated Rail Corporation |
| Rochester and Honeoye Valley Railroad | LV | 1888 | 1895 | Rochester Southern Railroad |
| Rochester, Hornellsville and Lackawanna Railroad | PS&N | 1886 | 1889 | Lackawanna and Southwestern Railroad |
| Rochester, Hornellsville and Pine Creek Railroad | PRR | 1872 | 1876 | Geneva, Hornellsville and Pine Creek Railway |
| Rochester and Lake Beach Railroad | NYC | 1888 | 1888 | Rome, Watertown and Ogdensburg Terminal Railroad |
| Rochester and Lake Ontario Railroad | NYC | 1852 | 1855 | New York Central Railroad |
| Rochester, Lockport and Niagara Falls Railroad | NYC | 1850 | 1853 | New York Central Railroad |
| Rochester, New York and Pennsylvania Railroad | PRR, PS&N | 1881 | 1916 | Allegany Central Railroad, Western New York and Pennsylvania Railway |
| Rochester, Nunda and Pennsylvania Railroad | PRR, PS&N | 1870 | 1877 | Rochester, Nunda and Pittsburgh Railroad |
| Rochester, Nunda and Pennsylvania Extension Railroad | PS&N | 1872 | 1872 | Rochester, Nunda and Pennsylvania Railroad |
| Rochester, Nunda and Pittsburgh Railroad | PRR | 1877 | 1881 | Rochester, New York and Pennsylvania Railroad |
| Rochester and Ontario Belt Railway | NYC | 1882 | 1887 | Rochester and Lake Beach Railroad |
| Rochester and Pine Creek Railroad | B&O | 1870 | 1877 | Silver Lake Railroad |
| Rochester and Pittsburgh Railroad | B&O | 1881 | 1885 | Buffalo, Rochester and Pittsburgh Railroad |
| Rochester Southern Railroad | LV | 1895 | 1903 | Lehigh Valley Railway |
| Rochester and Southern Railroad | LV | 1895 | 1895 | Rochester Southern Railroad |
| Rochester and State Line Railroad | B&O | 1869 | 1881 | Rochester and Pittsburgh Railroad |
| Rochester and Syracuse Railroad | NYC | 1850 | 1853 | New York Central Railroad |
| Rockaway Railway | LI | 1871 | 1872 | South Side Railroad of Long Island |
| Rockland Central Railroad | NYC | 1870 | 1873 | Jersey City and Albany Railroad |
| Rockland Central Extension Railroad | NYC | 1872 | 1872 | Rockland Central Railroad |
| Rome and Clinton Railroad | NH | 1869 | 1944 | New York, Ontario and Western Railway |
| Rome, Watertown and Ogdensburg Railroad | NYC | 1861 | 1913 | New York Central and Hudson River Railroad |
| Rome, Watertown and Ogdensburg Terminal Railroad | NYC | 1886 | 1890 | Rome, Watertown and Ogdensburg Railroad |
| Rondout and Oswego Railroad | NYC | 1866 | 1872 | New York, Kingston and Syracuse Railroad |
| Rutland Railroad | RUT | RUT | 1899 | 1950 | Rutland Railway |
| Rutland Railway | RUT | RUT | 1950 | 1961 | New York Central Railroad |
| Rutland–Canadian Railroad | RUT | 1898 | 1901 | Rutland Railroad |
| Rutland and Washington Railroad | D&H | 1850 | 1865 | Troy, Salem and Rutland Railroad |
| Sackets Harbor and Ellisburg Railroad | 1851 | 1858 | Sackett's Harbor, Rome and New York Railroad |
| Sackett's Harbor, Rome and New York Railroad | 1860 | 1862 | N/A |
| Sackets Harbor and Saratoga Railroad | D&H | 1852 | 1857 | Lake Ontario and Hudson River Railroad |
| St. Lawrence Railroad | SLAW | 1977 | 1990 | St. Lawrence and Raquette River Railroad |
| St. Lawrence and Adirondack Railroad | NYC | 1891 | 1892 | Mohawk and Malone Railway |
| St. Lawrence and Adirondack Railway | NYC | 1895 | Still exists as a nonoperating subsidiary of CSX Transportation |
| St. Lawrence and Hudson Railway | STLH | CP | 1996 | 2001 | Canadian Pacific Railway |
| St. Lawrence and Raquette River Railroad | SLRR | 1990 | 1998 | New York and Ogdensburg Railway |
| Salamanca, Bradford and Allegheny River Railroad | PRR | 1880 | 1881 | Buffalo, Pittsburgh and Western Railroad |
| Saranac and Lake Placid Railroad | D&H | 1890 | 1903 | Chateaugay and Lake Placid Railway |
| Saratoga and Fort Edward Railroad | D&H | 1832 | | Saratoga and Washington Railroad |
| Saratoga and Hudson River Railroad | NYC | 1864 | 1867 | New York Central Railroad |
| Saratoga Lake Railway | B&M | 1880 | 1886 | Troy, Saratoga and Northern Railroad |
| Saratoga and Mount McGregor Railway | 1896 | 1897 | Saratoga Northern Railway |
| Saratoga, Mount McGregor and Lake George Railroad | 1882 | 1888 | Mount McGregor Railroad |
| Saratoga Northern Railway | 1899 | 1901 | Hudson Valley Railway (electric) |
| Saratoga and St. Lawrence Railroad | 1885 | 1897 | Bombay and Moira Railroad |
| Saratoga and Schenectady Railroad | D&H | 1831 | |
| Saratoga and Schuylerville Railroad | 1945 | 1956 | N/A |
| Saratoga and Washington Railroad | D&H | 1834 | 1855 | Saratoga and Whitehall Railroad |
| Saratoga and Whitehall Railroad | D&H | 1855 | 1868 | Rensselaer and Saratoga Railroad |
| Schenectady and Duanesburgh Railroad | D&H | 1873 | 1903 | Delaware and Hudson Company |
| Schenectady and Margaretville Railroad | 1906 | 1907 | Delaware and Eastern Railway |
| Schenectady and Mechanicville Railroad | D&H | 1867 | |
| Schenectady and Susquehanna Railroad | D&H | 1869 | 1873 | Schenectady and Duanesburgh Railroad |
| Schenectady and Troy Railroad | NYC | 1836 | 1853 | New York Central Railroad |
| Schoharie Valley Railroad | D&H | 1865 | 1874 | Schoharie Valley Railway |
| Schoharie Valley Railway | D&H | 1880 | 1941 | N/A |
| Schuylerville and Upper Hudson Railroad | B&M | 1869 | 1877 | Mechanicville and Fort Edward Railroad |
| Scottsville and LeRoy Railroad | 1836 | | N/A |
| Sea Beach Railway | 1896 | 1912 | New York Consolidated Railroad | Electrified in 1898 |
| Sea Beach and Brighton Railroad | 1886 | 1892 | Brighton and Bensonhurst Railroad |
| Seneca County Railway | LV | 1891 | 1903 | Lehigh Valley Railway |
| Sharon and Ceres Terminal Railroad | 1904 | 1904 | New York and Pennsylvania Railway |
| Shawmut Connecting Railroad | PS&N | 1900 | 1905 | Pittsburg, Shawmut and Northern Railroad |
| Silver Creek and Dunkirk Railway | NYC | 1890 | 1894 | Lake Shore and Michigan Southern Railway |
| Silver Lake Railroad | B&O | 1877 | 1886 | Silver Lake Railway |
| Silver Lake Railroad | B&O | 1869 | Rochester and Pine Creek Railroad |
| Silver Lake Railway | B&O | 1886 | 1910 | Buffalo, Rochester and Pittsburgh Railway |
| Skaneateles Railroad | 1866 | 1941 | Skaneateles Short Line Railroad |
| Skaneateles Railroad | 1836 | 1841 | Skaneateles and Jordan Railroad |
| Skaneateles and Jordan Railroad | 1841 | 1851 | N/A |
| Skaneateles Short Line Railroad | SSL | 1940 | 1981 | N/A |
| Smithtown and Port Jefferson Railroad | LI | 1870 | 1892 | Long Island Railroad North Shore Branch |
| Sodus Bay and Southern Railroad | PRR | 1882 | 1886 | Elmira and Lake Ontario Railroad |
| Sodus Point and Southern Railroad | PRR | 1852 | 1875 | Ontario Southern Railroad |
| South Brooklyn Railroad and Terminal Company | 1887 | 1899 | South Brooklyn Railway |
| South Brooklyn Railway | SBK | 1900 | | Electric until 1961 |
| South Brooklyn and Flatbush Railroad | 1885 | 1887 | South Brooklyn Railroad and Terminal Company |
| South Side Railroad of Long Island | LI | 1860 | 1874 | Southern Railroad of Long Island |
| Southern Railroad of Long Island | LI | 1874 | 1880 | Brooklyn and Montauk Railroad |
| Southern Central Railroad | LV | 1865 | 1895 | Lehigh and New York Railroad |
| Southern Hempstead Branch Railroad | LIRR | 1875 | 1882 | Stewart Railroad |
| Southern New York Railroad | 1888 | 1970 | N/A |
| Southern Westchester Railroad | 1871 | 1872 | New York, Housatonic and Northern Railroad |
| Southfield Branch Railroad | 1868 | 1894 | N/A |
| Springville and Sardinia Railroad | 1878 | 1886 | N/A |
| Spuyten Duyvil and Port Morris Railroad | NYC | 1867 | 1913 | New York Central and Hudson River Railroad |
| Staten Island Railroad | SIRC | B&O | 1971 | 1991 | N/A |
| Staten Island Railroad | B&O | 1851 | 1872 | Staten Island Railway |
| Staten Island Railway | B&O | 1873 | 1944 | Staten Island Rapid Transit Railway |
| Staten Island Rapid Transit Railroad | B&O | 1880 | 1899 | Staten Island Rapid Transit Railway |
| Staten Island Rapid Transit Railway | SIR | B&O | 1899 | 1971 | Staten Island Railroad |
| Sterling Mountain Railway | 1864 | 1955 | N/A |
| Stewart Railroad | LIRR | 1873 | 1892 | Long Island Rail Road |
| Stony Clove and Catskill Mountain Railroad | NYC | 1881 | 1901 | Ulster and Delaware Railroad |
| Suffern Railroad | ERIE | 1907 | 1907 | Erie and Jersey Railroad |
| Suspension Bridge and Erie Junction Railroad | ERIE | 1868 | 1896 | Erie Railroad |
| Syracuse and Baldwinsville Railroad | DL&W | 1886 | 1891 | Syracuse and Baldwinsville Railway |
| Syracuse and Baldwinsville Railway | DL&W | 1891 | | N/A |
| Syracuse and Binghamton Railroad | DL&W | 1851 | 1856 | Syracuse and Southern Railroad |
| Syracuse, Binghamton and New York Railroad | DL&W | 1857 | 1945 | Delaware, Lackawanna and Western Railroad |
| Syracuse and Chenango Railroad | NYC | 1873 | 1877 | Syracuse, Chenango and New York Railroad |
| Syracuse and Chenango Valley Railroad | NYC | 1868 | 1873 | Syracuse and Chenango Railroad |
| Syracuse, Chenango and New York Railroad | NYC | 1877 | 1883 | Syracuse, Ontario and New York Railway |
| Syracuse, Geneva and Corning Railway | NYC | 1875 | 1909 | Geneva, Corning and Southern Railroad |
| Syracuse Junction Railroad | NYC | 1873 | 1879 | New York Central and Hudson River Railroad |
| Syracuse Northern Railroad | NYC | 1868 | 1875 | Syracuse and Northern Railroad |
| Syracuse and Northern Railroad | NYC | 1875 | 1875 | Rome, Watertown and Ogdensburg Railroad |
| Syracuse Northwestern Railroad | NYC | 1874 | 1875 | Syracuse, Phoenix and Oswego Railroad |
| Syracuse, Ontario and New York Railway | NYC | 1883 | 1891 | West Shore Railroad |
| Syracuse, Phoenix and Oswego Railroad | NYC | 1871 | 1885 | Syracuse, Phoenix and Oswego Railway |
| Syracuse, Phoenix and Oswego Railway | NYC | 1885 | 1889 | Rome, Watertown and Ogdensburg Railroad |
| Syracuse and Southern Railroad | DL&W | 1856 | 1857 | Syracuse, Binghamton and New York Railroad |
| Syracuse and Utica Railroad | NYC | 1836 | 1853 | New York Central Railroad |
| Syracuse and Utica Direct Railroad | NYC | 1853 | 1853 | New York Central Railroad |
| Terminal Railway of Buffalo | NYC | 1895 | 1914 | New York Central Railroad |
| Ticonderoga Railroad | D&H | 1889 | 1957 | Delaware and Hudson Railroad |
| Tioga Railroad | ERIE | 1876 | 1885 | New York, Lake Erie and Western Railroad |
| Tioga Central Railroad | TIOC | 1987 | 1992 | Owego and Harford Railway |
| Tioga Coal, Iron Mining and Manufacturing Company | NYC | 1833 | 1851 | Corning and Blossburg Railroad |
| Tivoli Hollow Railroad | NYC | 1893 | 1913 | New York Central and Hudson River Railroad |
| Tonawanda Railroad | NYC | 1832 | 1850 | Buffalo and Rochester Railroad |
| Tonawanda Island Railroad | TIRL | 1983 | 1996 | N/A |
| Tonawanda Island Bridge Company | NYC | 1883 | 1913 | New York Central and Hudson River Railroad |
| Tonawanda Valley Railroad | 1880 | 1881 | Tonawanda Valley and Cuba Railroad |
| Tonawanda Valley and Cuba Railroad | 1881 | 1886 | Attica and Freedom Railroad |
| Tonawanda Valley Extension Railroad | 1880 | 1881 | Tonawanda Valley and Cuba Railroad |
| Troy and Bennington Railroad | B&M | 1851 | 1946 | Boston and Maine Railroad |
| Troy and Boston Railroad | B&M | 1848 | 1887 | Fitchburg Railroad |
| Troy and Greenbush Railroad | NYC | 1845 | 1976 | Consolidated Rail Corporation |
| Troy and Rutland Railroad | D&H | 1849 | 1865 | Troy, Salem and Rutland Railroad |
| Troy, Salem and Rutland Railroad | D&H | 1865 | 1868 | Rensselaer and Saratoga Railroad |
| Troy, Saratoga and Northern Railroad | B&M | 1886 | 1892 | Fitchburg Railroad |
| Troy Union Railroad | B&M/ D&H/ NYC | 1851 | 1964 | N/A |
| Tunesassa and Bradford Railroad | 1905 |
| Ulster and Delaware Railroad | NYC | 1875 | 1932 | New York Central Railroad |
| Unadilla Valley Railway | UV | 1890 | 1960 | N/A |
| Union Railroad | ERIE | 1851 | 1946 | Erie Railroad |
| Union Railroad | DL&W | 1856 | 1858 | Syracuse, Binghamton and New York Railroad |
| Union Terminal Railroad of Buffalo | PRR | 1884 | 1917 | Western New York and Pennsylvania Railway |
| Union Village and Johnsonville Railroad | D&H | 1866 | 1874 | Greenwich and Johnsonville Railroad |
| United States and Canada Railroad | CN | 1883 | 1960 | Canadian National Railway |
| Upper Hudson Railroad | B&M | 1872 | 1872 | Schuylerville and Upper Hudson Railroad |
| Utica and Black River Railroad | NYC | 1860 | 1913 | New York Central and Hudson River Railroad |
| Utica, Chenango and Cortland Railroad | DL&W | 1870 | 1883 | Erie and Central New York Railway |
| Utica, Chenango and Susquehanna Valley Railway | DL&W | 1866 | 1945 | Delaware, Lackawanna and Western Railroad |
| Utica City Railroad | NH | 1862 | 1866 | Utica and Waterville Railroad |
| Utica, Clinton and Binghamton Railroad | NH | 1868 | 1942 | New York, Ontario and Western Railway |
| Utica, Horseheads and Elmira Railroad | LV | 1870 | 1871 | Utica, Ithaca and Elmira Railroad |
| Utica, Ithaca and Elmira Railroad | LV | 1871 | 1878 | Utica, Ithaca and Elmira Railway |
| Utica, Ithaca and Elmira Railway | LV | 1878 | 1884 | Elmira, Cortland and Northern Railroad |
| Utica and Schenectady Railroad | NYC | 1833 | 1853 | New York Central Railroad |
| Utica and Unadilla Valley Railroad | 1888 | 1895 | Unadilla Valley Railway |
| Utica and Waterville Railroad | NH | 1866 | 1868 | Utica, Clinton and Binghamton Railroad |
| Valley Railroad | DL&W | 1869 | 1945 | Delaware, Lackawanna and Western Railroad |
| Vermont and Canada Railroad | CN | 1845 | 1891 | Central Vermont Railroad |
| Vermont Central Railroad | CN | 1870 | 1873 | Central Vermont Railroad |
| Vermont Central Railroad | CN | 1849 | 1855 | N/A | Leased the Vermont and Canada Railroad |
| Wabash Railroad | WAB | 1898 | 1915 | Wabash Railway |
| Wabash Railroad | WAB | WAB | 1942 | 1964 | Norfolk and Western Railway |
| Wabash Railway | WAB | 1915 | 1942 | Wabash Railroad |
| Wallkill Valley Railroad | NYC | 1877 | 1952 | New York Central Railroad |
| Wallkill Valley Railway | NYC | 1866 | 1877 | Wallkill Valley Railroad |
| Warwick Valley Railroad | L&HR | 1860 | 1882 | Lehigh and Hudson River Railway |
| Watertown and Rome Railroad | NYC | 1832 | 1861 | Rome, Watertown and Ogdensburg Railroad |
| Waverly and State Line Railway | LV | 1867 | 1903 | Lehigh Valley Railway |
| Wellsville, Addison and Galeton Railroad | WAG | 1954 | 1973 | N/A |
| Wellsville, Bradford and Eldred Railroad | 1881 | 1893 | N/A (operated by Bradford, Eldred and Cuba Railroad) |
| Wellsville and Buffalo Railroad | 1915 | 1916 | N/A |
| Wellsville, Coudersport and Pine Creek Railroad | B&O | 1881 | 1954 | Buffalo and Susquehanna Railroad |
| West Brooklyn Railroad | 1887 | 1889 | N/A (operated by Brooklyn, Bath and West End Railroad) |
| West Davenport Railroad | D&H | 1891 | 1891 | Cooperstown and Charlotte Valley Railroad |
| West Shore Railroad | NYC | 1885 | 1952 | New York Central Railroad |
| West Shore Hudson River Railroad | NYC | 1867 | 1877 | New York, West Shore and Chicago Railroad |
| West Side and Yonkers Railway | NYC | 1879 | 1887 | New York City and Northern Railroad |
| West Troy and Green Island Railroad | D&H | 1870 | |
| Westchester Railway | 1881 | N/A (never completed) |
| Western New York Railway | PRR | 1895 | 1895 | Western New York and Pennsylvania Railway |
| Western New York and Pennsylvania Railroad | PRR | 1887 | 1895 | Western New York and Pennsylvania Railway |
| Western New York and Pennsylvania Railway | PRR | 1895 | 1955 | Penndel Company |
| Western New York and Pennsylvania Railway of New York | PRR | 1887 | 1887 | Western New York and Pennsylvania Railroad |
| Western Vermont Railroad | RUT | 1845 | 1865 | Bennington and Rutland Railroad |
| Wharton Valley Railway | NH | 1888 | 1942 | N/A |
| Whitehall and Plattsburgh Railroad | D&H | 1866 | 1873 | New York and Canada Railroad |
| Whitestone and Westchester Railroad | LI | 1871 | 1887 | Long Island City and Flushing Railroad |
| Williamsport and Elmira Railroad | PRR | 1850 | 1860 | Elmira and Williamsport Railroad |
| Williamstown and Redfield Railroad | 1865 | | N/A |
| Windsor Beach and Ontario Railroad | NYC | 1887 | 1888 | Rome, Watertown and Ogdensburg Terminal Railroad |
| Yonkers Rapid Transit Railway | NYC | 1879 | 1887 | New York and Northern Railway |
1. ^This is one or more of the Class I railroads that the railroad became part of, if any.