The 1939–40 season was the 42nd in the history of the Southern League.
The league was split into two sections, Eastern and Western as part of an emergency war-time competition.
A championship play-off between the two clubs was drawn 3–3 and they were declared joint champions.
[2] After this season, the Southern Football League did not resume until World War II had ended in 1945.
The Western Section featured three new clubs: