When World War II was declared in 1939, it had a negative effect on association football; competitions were suspended and players signed up to fight, resulting in the deaths of many players.
The Republic of Austria had ceased to exist with the Anschluss in 1938 and the Austrian league had become a part of the German football league system, under the name of Gauliga Ostmark. League football resumed in a now independent Austria again in 1945.
The 1939–1940 season was the 65th season of competitive football in England. In September 1939, shortly after World War II was declared, most football competitions were abandoned as the country's attention turned to the war effort. Regional league competitions were set up instead; appearances in these tournaments do not count in players' official records. A few leagues, such as the Northern League, did manage to complete a season, but more than half of the teams were unable to fulfil all their fixtures and resigned. Many footballers signed up to fight in the war and as a result many teams were depleted, and fielded guest players instead – Crystal Palace fielded 186 different players during the seven wartime seasons. The FA Cup was resumed for the 1945-46 season and The Football League for the 1946-47 season.
The 1939-40 season started in August 1939, but with the outbreak of the Second World War shortly after, league football was suspended. It only resumed at the end of October, with a number of local city-championships having been played to bridge the gap. As the war progressed, top-division football became more regionalised. It also expanded into occupied territories, some of them annexed into Greater Germany, increasing the number of tier-one Gauligas considerably from the original 16 in 1933. The last German championship was played in 1944 and won by Dresdner SC, but the last official league game was played as late as 23 April 1945, being the FC Bayern Munich versus TSV 1860 Munich derby in the Gauliga Oberbayern, ending 3-2. The final years of league football saw the rise of military teams, like LSV Hamburg, who reached the 1944 German championship final, since most top-players were drafted into the German armed forces and ended up playing for these sides. Representative teams like the Rote Jäger also had a number of German internationals playing for them.