The 1990–91 season was the 76th season of the Isthmian League, an English football competition featuring semi-professional and amateur clubs from London, East and South East England.
The league consisted of three divisions. The Second Division was divided into two sections. At the end of the season, Division Two North and Division Two South were merged into a single Division Two, and Division Three was formed.
The Premier Division consisted of 22 clubs, including 19 clubs from the previous season and three new clubs:
Division One consisted of 22 clubs, including 16 clubs from the previous season and six new clubs:
Two clubs relegated from the Premier Division:
Two clubs promoted from Division Two North:
Two clubs promoted from Division Two South:
Division Two North consisted of 22 clubs, including 19 clubs from the previous season and three new clubs:
At the end of the season Division Two North and Division Two South were merged into single Division Two and also Division Three was formed. Finchley merged with Wingate to form Wingate & Finchley who took Wingate's place in the South Midlands League Premier Division, while Basildon United resigned to the Essex Senior League.
Division Two South consisted of 22 clubs, including 19 clubs from the previous season and three new clubs:
At the end of the season Division Two North and Division Two South were merged into single Division Two and also Division Three was formed.
Before the next season started Feltham merged with the Hellenic League side Hounslow F.C. to create Feltham & Hounslow Borough F.C.