The 1946–47 season was the 32nd in the history of the Isthmian League, an English football competition.
Leytonstone were champions, winning their fourth Isthmian League title.
| Competition: | Isthmian League |
| Season: | 1946–47 |
| Winners: | Leytonstone |
| Matches: | 182 |
| Total Goals: | 832 |
| Prevseason: | 1945–46 |
| Nextseason: | 1947–48 |