The 1928–29 season was the thirty-first in the history of the Southern League.
The league consisted of Eastern and Western Divisions.
Plymouth reserves were declared Southern League champions after winning a championship play-off at Kettering 4-2.
Two clubs (both from the Eastern Division) left the league at the end of the season.
Newly elected team: Three Southern League clubs, Aldershot Town, Thames Association and Kettering Town, applied to join the Football League.