The 1959–60 Southern Football League season saw the league split into a Premier Division and Division One, the first time the league had had two hierarchical divisions since 1919–20. Bath City won the championship, whilst Clacton Town, Romford, Folkestone Town and Guildford City were all promoted to the Premier Division. Eleven Southern League clubs applied to join the Football League at the end of the season, but none were successful.
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Premier Division
1 The system of using goal average to separate two teams tied on points was used up until the 1976-77 season.
2 The points system: 2 points for a win, 1 point for a draw and 0 points for losing.
Football League elections
Eleven Southern League clubs (including Guildford City and Romford from Division One) applied for election to the Football League. Although none were successful, Peterborough United were elected at the expense of Gateshead.
Division One
Division One featured ten new clubs: