The 2012–13 season was the 98th season of the Isthmian League, which is an English football competition featuring semi-professional and amateur clubs from London, East and South East England.
Initially, Carshalton Athletic and Hastings United were relegated, but Thurrock were subsequently deducted three points for fielding a suspended player on the second day of the season.
Ilford finished bottom of the table and were relegated from the division after seven seasons.
Division One South consisted of 22 clubs, including 17 clubs from the previous season, and five new clubs: Dulwich Hamlet won the division and were promoted to the Premier Division along with play-off winners Maidstone United, who returned after two seasons of absence.
Walton Casuals finished bottom of the table, but were reprieved for the second time in four seasons.