The 1946–47 Southern Football League season was the 44th in the history of the league, an English football competition.
Clubs missed previous season: Newly elected clubs: Gillingham were champions, winning their first Southern League title.
At the end of the season Millwall resigned from the league.
Barry Town, Bath City, Chelmsford City, Colchester United, Gillingham, Gravesend & Northfleet, Guildford City, Merthyr Tydfil, Worcester City and Yeovil Town were amongst 27 non-League clubs to apply for election to the Football League.
However, as the two clubs relegated from Division Two to the regional divisions Three were both from the south, the Football League secretary had suggested that electing new members could create an imbalance in the divisions' geographical boundaries, and that instead all four clubs (Halifax, Mansfield, Norwich and Southport) should be re-elected en bloc.