| AIRLINE | IATA | ICAO | CALLSIGN | IMAGE | COMMENCED OPERATIONS | CEASED OPERATIONS | NOTES |
|---|
| Air Central | NV | CRF | AIR CENTRAL | 1988 | 2010 | Merged with Air Next and Air Nippon Network to form ANA Wings |
| Air Hokkaido | ADK | AIR DREAM | 1994 | 2006 |
| Air Next | 7A | NXA | BLUE-DOLPHIN | 2004 | 2010 | Merged with Air Central and Air Nippon Network to form ANA Wings |
| Air Nippon | EL | ANK | ANK AIR | 1987 | 2012 | Merged into All Nippon Airways |
| Air Nippon Network | EH | AKX | ALPHA WING | 2002 | 2010 | Merged with Air Central and Air Next to form ANA Wings |
| AirAsia Japan (Part 1) | DJ | WAJ | WING ASIA | 2011 | 2013 |
| All Nippon AW | NH | ANA | ANA / Zen Nippon Kuyu | 1958 | 2002 | renamed/merged to: All Nippon Airways |
| ANA & JP Express | 9N | AJV | AYJAY CARGO | 2006 | 2010 | Merged into Air Japan |
| Fuji Air Lines | [3] | 1952 | 1964 | Merged with Nitto Airlines and North Japan Airlines to form Japan Domestic Airlines |
| Fujita Airlines | [4] | 1956 | 1963 | Merged into All Nippon Airways |
| Galaxy Airlines | J7 | GXY | GALAX | 2005 | 2008 |
| Harlequin Air | JH | HLQ | HARLEQUIN | 1997 | 2005 | Affiliate of Japan Air System : now part of Japan Airlines |
| Imperial Japanese Airways | 1938 | 1945 |
| Japan Airlines(JAL) | Japanese AL | 1951 | 1953 | renamed/merged to : Japan Airlines |
| Japan Airlines (JAL) | JL | JAL | Japan AL / Nihon Koku | 1953 | 1989 | renamed/merged to : Japan Airlines |
| Japan Airlines (JAL) | JL | JAL | Japan AL / Nihon Koku | 1989 | 2004 | renamed/merged to : Japan Airlines |
| Japan Airlines (JAL) | JL | JAL | Japan AL Int'l | 2004 | 2011 | renamed/merged to : Japan Airlines |
| Japan Airlines Domestic | JL | JLJ | J-BIRD | 1964 | 2006 | Merged into Japan Airlines |
| Japan Asia Airways | EG | JAA | ASIA | 1975 | 2008 | Merged into Japan Airlines |
| Japan Domestic Airlines | [5] | 1964 | 1971 | Merged with Toa Airways to form Toa Domestic Airlines |
| JAL Express | JC | JEX | JANEX | 1997 | 2014 | Integrated into Japan Airlines |
| JALways | JO | JAZ | JALWAYS | 1991 | 2010 | Merged into Japan Airlines |
| Japan Air System | JD | JAS | JAPAN AIR | 1988 | 2004 | Rebranded as Japan Airlines Domestic |
| Japan Air Transport | 1928 | 1938 | Merged into Imperial Japanese Airways |
| Japan Universal System Transport | YU | JST | 1991 | 1996 |
| Kansai Airlines |
| Kyokushin Air | 2008 |
| Link Airs | 2014 | Went bankrupt : Never launched |
| Nakanihon Airlines | 1998 | 2005 | Commuter division of Nakanihon Air Service, rebranded as Air Central |
| Nitto Airlines | 1955 | 1964 | Merged with Fuji Air Lines and North Japan Airlines to form Japan Domestic Airlines |
| North Japan Airlines | [6] | 1962 | 1964 | Merged with Fuji Air Lines and Nitto Airlines to form Japan Domestic Airlines |
| Orange Cargo | ORJ | ORANGE CARGO | 2002 | 2004 | Went bankrupt |
| Skynet Asia Airways | LQ | SNJ | 1997 | 2011 | Rebranded as Solaseed Air |
| Southwest Air Lines | NU | SWL | 1967 | 1993 | Rebranded as Japan Transocean Air |
| Toa Airways | TAW | 1953 | 1971 | Merged with Japan Domestic Airlines to form Toa Domestic Airlines |
| Toa Domestic Airlines | JD | TDA | 1971 | 1988 | Rebranded as Japan Air System |
1. ^{{cite web|url=http://www.ch-aviation.com/|website=ch-aviation.com|title=The World's leading Airline Intelligence Provider since 1998|accessdate=2018-12-02}}
2. ^{{cite web|url=http://www.aerotransport.org/|website=aerotransport.org|title=Since 1997, ATDB is the only service providing an accurate global and permanently updated details of all worldwide transport aircraft, airlines, private and government operators - and leasing companies.|accessdate=2018-12-02}}
3. ^Fuji Air Lines. {{cite web|url=https://www.airliners.net/photo/Fuji-Airlines/Convair-240-26/1033863|title=Fuji Air Lines.|accessdate=2018-12-02}}
4. ^Fujita Airlines. {{cite web|url=https://www.airliners.net/photo/Fuji-Airlines/Convair-240-26/1033863|title=Fujita Airlines.|accessdate=2018-12-02}}
5. ^{{cite web|url=http://aerobernie.bplaced.net/Fotos%2021/JDA-727.jpg|title=Japan Domestic Airlines.|accessdate=2018-12-02}}
6. ^North Japan Airlines. {{cite web|url=https://jjpostcards.com/en/postcards/27719-north-japan-nja-cv-240.html|title=North Japan Airlines.|accessdate=2018-12-02}}
{{List of airlines}}{{List of defunct airlines}}