Wolves made an indifferent start to the 1939-40 season, drawing 2-2 with Arsenal, 0-0 at Grimsby and losing 1-2 at Blackpool. Three games into the season war was declared and the Football League was suspended.

After a three week gap the Football League was re-organised into war-time regional leagues, restricting the distances that teams had to travel. Wolves at first played in the Midland section, later they joined the Southern section.

Wolves didn't particpate in the 1940-41 season, when Molineux became the headquarters for the nation's Air Raid Precautions Unit.

Wolves won the Midland Regional League Championship in 1939-40 and in the 1941-42 season they won the Football League War Cup (beating Sunderland on aggregate in the two-legged final).

During the war teams fielded sides using whatever players they could find, including guest players, youngsters and over-age professionals. Stan Cullis played many games for the army when abroad and also often played for Aldershot when he was based at the army camp there.

Eric Robinson, who played for Wolves in the 1941-42 League War Cup final unfortunately died three months later (aged 23). He drowned while taking part in military exercises. A year later another Wolves player, Joe Rooney, was killed in Italy aged 24.

Billy Wright made his debut as a 15 year old player during the war years. Bert Williams, one of Wolves most famous keepers was signed from Walsall in 1945 - Bert had been capped for England during the war.

Wolves were knocked out of the 1944-45 War-time cup in a two-legged semi-final with Bolton Wanderers. The war ended between the first and second legs, meaning that Dennis Westcott could play in the second leg - returning from army service in Bremen. Alex McIntish, who had been reported missing belived killed only afew weeks earlier, returned from prisioner-of-war camp to also play. Neither Westcott nor McIntosh could prevent Wolves losing 3-4 on aggregate.

The 1945-46 season was an interim season and Wolves played in the Southern league. They played 42 matches, winning 20, drawing 11 and losing 11. Wolves ended up in 6th place with 51 points. They were knocked out of the FA Cup by Charlton, having earlier beat Lovell's Athletic.