| Flag | Date | Use | Description |
|---|
| ?–present | Armed Forces Flag | . Ratio: 1:1 |
| ?–present | Army Flag | . Ratio: 2:3 |
| ?–present | Airforce Flag | White flag charged with the State flag in the canton and with stylized azure wings and double cross of Jogaila family in lower right quarter. The cross of Jogaila family is white bordered with two black bends. Ratio: 1:2 |
| 1992–present | Naval ensign | White with a dark blue St. George-style cross throughout and the Lithuanian tricolor in the canton. Ratio: 1:2 |
| 1992–2004 | Naval jack | White with a circular badge showing the stylized Columns of Gediminas on a red field, with a dark blue anchor behind the badge. Ratio: 1:2 |
| 2004–present | Naval jack | Identical to a historical state flag of Lithuania. Ratio: 3:5 |
| 1992–present | The Flag of Commander-in-Chief of the Armed Forces | White flag with the national tricolour in the canton and three sixpointed stars set in rasing diagonal in the fly half. The stars are sixpointed segmented with black lines and with white border fimbriated with red |
| 1992–present | Chief of Staff's Flag | Flag similar to CinC Armed Forces, but with two stars only. |
| 1992–present | Commander Naval Armed Forces | Flag similar to CinC Armed Forces, but with a single star only. |
| ?–present | Brigade Commander's flag | Pennat consisting of the national flag at hoist and tapering swallow-tailed white part at fly, continuing two red stars (of the same shape as in the previous flags) next to each other. Ratio: 1:5 |
| ?–present | Division Commander | Same as Brigade Commander's flag, but with single star. Ratio: 1:5 |
| ?–present | Group Commander | Same as Brigade Commander's flag, but without the stars. Ratio: 1:5 |
| ?–present | Masthead Pennant | Rectangular pennant with swallow-tail, national tricolour at hoist (1:4) and blue fly. Total flag ratio: 1:20 |
| 1946–1991 | Flag of the Soviet Army | Used under Soviet occupation. |
| 1940–1950 | Ensign of the Naval Fleet of the USSR | Used under Soviet occupation. |
| 1950–1991 | Ensign of the Naval Fleet of the USSR | Slight modification from previous design. Used under Soviet occupation. |
| Flag | Date | Use | Description |
|---|
| 1988–2004 | State flag and civil ensign | Ratio: 1:2 |
| 1953–1988 | Flag of the Lithuanian SSR |
| 1944–1953 | Soviet occupation (Lithuanian SSR) | |
| Flag of the Soviet Union.svg}} | 1980–1991 | Flag of the Soviet Union |
| Flag of the Soviet Union (1955-1980).svg}} | 1955–1980 | Flag of the Soviet Union |
| Flag of the Soviet Union (1936-1955).svg}} | 1944–1955 | Flag of the Soviet Union |
| 1941–1944 | German occupation |
| Flag of the Soviet Union (1936-1955).svg}} | 1940–1941 | Flag of the Soviet Union |
| 1940 August 3 – 1941 | Soviet occupation from 3 July 1940 till 22 June 1941 (Lithuanian SSR) |
| 1918–1940 | State flag and civil ensign of Republic of Lithuania |
| 17th century | Royal Banner of Poland–Lithuania |
| 15th century | Royal Banner of Lithuania |
Each county of Lithuania has adopted a flag, each of them conforming to a pattern: a blue rectangle, with ten instances of the Cross of Vytis appearing in gold, acts as a fringe to the central feature of the flag, which is chosen by the county itself. Most of the central designs were adapted from the counties' coat of arms.