The 1986–87 season was the 72nd season of the Isthmian League, which is an English football competition featuring semi-professional and amateur clubs from London, East and South East England. League consisted of three divisions. The Second Division was divided into two sections.
Wycombe Wanderers won the league and returned to the Conference at the first attempt.
| Competition: | Isthmian League Premier Division |
| Season: | 1986–87 |
| Winners: | Wycombe Wanderers |
| Promoted: | Wycombe Wanderers |
| Relegated: | Walthamstow Avenue Worthing |
| Matches: | 462 |
| Total Goals: | 1348 |
| Prevseason: | 1985–86 |
| Nextseason: | 1987–88 |
The Premier Division consisted of 22 clubs, including 19 clubs from the previous season and three new clubs:
| Competition: | Isthmian League Division One |
| Season: | 1986–87 |
| Winners: | Leytonstone/Ilford |
| Promoted: | Leytonstone/Ilford Leyton-Wingate |
| Relegated: | Epsom & Ewell Finchley Maidenhead United Tilbury |
| Matches: | 462 |
| Total Goals: | 1311 |
| Prevseason: | 1985–86 |
| Nextseason: | 1987–88 |
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:
| Competition: | Isthmian League Division Two North |
| Season: | 1986–87 |
| Winners: | Chesham United |
| Promoted: | Chesham United Wolverton Town |
| Matches: | 462 |
| Total Goals: | 1326 |
| Prevseason: | 1985–86 |
| Nextseason: | 1987–88 |
Division Two North consisted of 22 clubs, including 16 clubs from the previous season and six new clubs:
| Competition: | Isthmian League Division Two South |
| Season: | 1986–87 |
| Winners: | Woking |
| Promoted: | Marlow Woking |
| Matches: | 420 |
| Total Goals: | 1248 |
| Prevseason: | 1985–86 |
| Nextseason: | 1987–88 |
Division Two South consisted of 21 clubs, including 18 clubs from the previous season and three new clubs: