The 1988–89 season was the 74th season of the Isthmian League, which is an English football competition featuring semi-professional and amateur clubs from London, East and South East England.
The league consisted of three divisions. Division Two was divided into two sections.
Leytonstone/Ilford were 1989 champions, winning their first Isthmian League title after renaming in 1983. In the summer of 1988, Oxford City had left the league after losing its ground. Also in the summer of 1988, Walthamstow Avenue merged into Leytonstone/Ilford: the new club regained Leytonstone/Ilford's name and place in the Premier Division.
| Competition: | Isthmian League Premier Division |
| Season: | 1988–89 |
| Winners: | Leytonstone/Ilford |
| Promoted: | Farnborough Town |
| Relegated: | Croydon Tooting & Mitcham United |
| Matches: | 462 |
| Total Goals: | 1236 |
| Highest Attendance: | 1,763 – Slough Town – Farnborough Town, (27 December) |
| Attendance: | 141,270 |
| Average Attendance: | 306 |
| Prevseason: | 1987–88 |
| Nextseason: | 1989–90 |
The Premier Division consisted of 22 clubs, including 19 clubs from the previous season and three new clubs:
At the end of the previous season First Division club Walthamstow Avenue merged into Leytonstone/Ilford. The new club started next season in the Premier Division under the name of the Premier Division club.
At the end of the season Leytonstone/Ilford were refused in promotion due to ground problems. The club changed its name into Redbridge Forest before the next season started.
Farnborough Town finished second and were promoted back to the Conference after four years in the Isthmian League.
| Competition: | Isthmian League Division One |
| Season: | 1988–89 |
| Winners: | Staines Town |
| Promoted: | Basingstoke Town Staines Town |
| Relegated: | Basildon United Bracknell Town Collier Row |
| Matches: | 420 |
| Total Goals: | 1170 |
| Highest Attendance: | 1,432 – Woking – Lewes, (6 May) |
| Attendance: | 85,740 |
| Average Attendance: | 204 |
| Prevseason: | 1987–88 |
| Nextseason: | 1989–90 |
Division One consisted of 21 clubs, including 15 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 One started the season one club short after Oxford City left the league after losing its ground, and Walthamstow Avenue merged into Leytonstone/Ilford at the end of the previous season.
| Competition: | Isthmian League Division Two North |
| Season: | 1988–89 |
| Winners: | Harlow Town |
| Promoted: | Harlow Town Purfleet |
| Relegated: | Wolverton Town |
| Matches: | 462 |
| Total Goals: | 1291 |
| Highest Attendance: | 512 – Stevenage Borough – Harlow Town, (14 January) |
| Attendance: | 57,239 |
| Average Attendance: | 124 |
| Prevseason: | 1987–88 |
| Nextseason: | 1989–90 |
Division Two North consisted of 22 clubs, including 18 clubs from the previous season and four new clubs:
| Competition: | Isthmian League Division Two South |
| Season: | 1988–89 |
| Winners: | Dorking |
| Promoted: | Dorking Whyteleafe |
| Matches: | 420 |
| Total Goals: | 1183 |
| Highest Attendance: | 365 – Whyteleafe – Dorking, (8 April) |
| Attendance: | 39,367 |
| Average Attendance: | 94 |
| Prevseason: | 1987–88 |
| Nextseason: | 1989–90 |
Division Two South consisted of 21 clubs, including 20 clubs from the previous season and one new club: