World War II commenced in Europe in September 1939, and had spread to the Pacific in December 1942. The Association had continued contesting the premiership in 1940 and 1941, but cancelled the 1942, 1943 and 1944 seasons when it became clear that the competition would distract from the war effort. On 12 June 1944, the Association decided that it would resume the premiership in 1945, even though the Pacific War would ultimately not end until late 1945. Two clubs – Brighton and Port Melbourne – both had obstacles to overcome to resume playing in the Association. Brighton had practically ceased to exist in either a playing or administrative capacity during the war, but upon it being confirmed that the Association was to resume, the club was able to assemble a football committee and make preparations for the season. Port Melbourne was unable to use North Port Oval as a home venue during the season as its surface was in need of repairs after having been commandeered and used as a vegetable garden as part of the war effort, so it secured Olympic Park as a home venue; but, unhappy with the arrangement, the club ultimately moved many of its games in the second half of the year to other Association grounds. The Victorian Football League had continued playing throughout the war, and approximately 200 VFA players had crossed to the rival competition. The Association delegates ruled that any players who did not return to the Association now that it had resumed competition would be suspended from the VFA for five years.
Premiership
The home-and-home season was played over twenty matches, before the top four clubs contested a finals series under the Page–McIntyre system to determine the premiers for the season.
Ladder
Finals
Awards
Ron Todd was the leading goalkicker for the season, kicking 179 goals in the home-and-home season and 188 goals overall. Todd broke Bob Pratt's Association record of 183 goals, achieved in 1941; his record also exceeded Western Australian forward George Doig's national record of 152 goals in a season, but it was not recognised as a national record because the Association was not playing under ANFC rules at the time. As of 2019 this remains the record for most goals in an Association season.
The Recorder Cup and V.F.A. Medal, which had been awarded to the best and fairest player in the Association, were replaced in 1945 by a single award known as the J. J. Liston Trophy, named after former Association president J. J. Liston who had died in 1944. Eric Beard won the award in 1945, polling 51 votes. Col Bencraft finished second with 36 votes, and J. Baker finished third with 32 votes.
On 28 April, Sandringham suffered its thirty-seventh consecutive loss, breaking the record of thirty-six set by Melbourne City in 1912–1913. Sandringham ultimately suffered forty-four consecutive defeats before defeating Oakleigh on 23 June, 10.12 d. 7.10. The club's last win had been on 25 May 1940 against Camberwell.
On 9 June, a crowd of 21,000 attended the match between Coburg and Williamstown at Coburg, setting a new record for the highest crowd ever at an Association home-and-home match.
In July, Brighton changed its colours from red and white to maroon and gold – in large part because their red and white guernseys were unusable after having shrunk in repeated washes.
A carnival was held at the St Kilda Cricket Ground on Sunday 2 September, with an attendance of 12,000 raising £426 for Prince Henry's Hospital. As part of the entertainment, a team of VFA umpires 8.9 defeated a team of VFL umpires 4.15 for the Ken LukeChallenge Cup; the match was played under League rules in the first half, and Association rules in the second half, with 's Jack Dyer and Coburg's Bob Atkinson serving as umpires for their respective codes.
Williamstown and Coburg visited Broken Hill in mid-October. On Saturday 20 October, Coburg 16.18 defeated Williamstown 12.8 in an exhibition match under Association rules; and on Sunday 21 October, a combined Coburg/Williamstown team 14.15 defeated a combined Broken Hill Football League team 12.12 under the League rules which were used in Broken Hill at the time. Both matches attracted large crowds.
