The 1903–04 season was the tenth in the history of Southern League. Division One, expanded up to 18 teams, was won by Southampton for the 6th time in history. Watford finished top of Division Two, earning automatic promotion, the first time that test matches had not been held. No clubs applied to join the Football League.
| Competition: | Southern Football League Division One |
| Season: | 1903–04 |
| Winners: | Southampton (6th title) |
| Promoted: | none |
| Relegated: | Kettering (resigned) |
| Matches: | 306 |
| Total Goals: | 809 |
| Prevseason: | 1902–03 |
| Nextseason: | 1904–05 |
A total of 18 teams contest the division, including 15 sides from previous season and three new teams.
Teams promoted from Division Two:
Newly elected team:
| Competition: | Southern Football League Division Two |
| Season: | 1903–04 |
| Winners: | Watford |
| Promoted: | Watford |
| Relegated: | Millwall II (resigned) Chesham Town (resigned) |
| Matches: | 110 |
| Total Goals: | 480 |
| Prevseason: | 1902–03 |
| Nextseason: | 1904–05 |
A total of eleven teams contest the division, including 4 sides from previous season, one team relegated from Division One and six new clubs in Division Two this season, all of which were reserve teams.
Teams promoted from Division Two:
Newly elected teams: