Blackpool sat atop the table at the time the abandonment occurred. The FA Cup Extra-Preliminary Round was played, but with hostilities declared before replays took place, that competition too was abandoned. Entry fees received for the 1939-40 Cup were honoured for the next Cup in 1945-46.
Many footballers signed up to fight in the war and as a result many teams were depleted, and fielded guest players instead. Regional league competitions were set up. Appearances in these tournaments do not count in players' official records. The FA Cup was resumed for the 1945-46 season and The Football League for the 1946-47 season.
After the abandonment of the football programme, the league was split into ten mini regional leagues. A national cup competition was also held.
| Competition | Winner |
|---|---|
| Midland League | Wolverhampton Wanderers |
| West League | Stoke City |
| North-East League | Huddersfield Town |
| North-West League | Bury |
| South League 'A' | Arsenal |
| South League 'B' | Queens Park Rangers |
| South League 'C' | Tottenham Hotspur |
| South League 'D' | Crystal Palace |
| South-West League | Plymouth Argyle |
| East Midland League | Chesterfield |
| Football League War Cup | West Ham United |