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.
A total of 23 teams contest the division, including 17 sides from previous season, one team relegated from The Football League and five new teams.
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. However, both League clubs were re-elected.[2]