The 2008–09 season was the 94th season of the Isthmian League, which is an English football competition featuring semi-professional and amateur clubs from London, East and South East England.
Harlow Town, Heybridge Swifts and Ramsgate were relegated to the Division One sections, while Margate, who also finished in the relegation zone, were reprieved due to the demotion of clubs higher up the pyramid.
Witham Town and Hillingdon Borough finished in the bottom two places and left the league.
Chipstead were reprieved from relegation due to the demotion of clubs higher up the pyramid.
‡ – Waltham Forest removed from competition, Witham Town reinstalled