The 1938–39 season was the 41st in the history of the Southern League.
Colchester United won the title.
[1] Three clubs applied to join the Football League, although none were successful.
The following season saw the league split into Eastern and Western sections as part an emergency war-time competition, after which the league was discontinued until the end of World War II.
Team relegated from 1937–38 Football League: Newly elected teams: Three Southern League clubs, Chelmsford City, Colchester United and Gillingham, applied to join the Football League.