World War II had commenced in Europe in September1939, and for the second consecutive season the Association opted to proceed with a full premiership season. Many Association players had enlisted in the war effort, and the Sandringham Football Club elected to operate on an amateur basis for the season.
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
Bob Pratt was the leading goalkicker for the season, kicking 165 goals in the home-and-home season and 183 goals overall. Pratt broke George Hawkins' Association record of 164 goals, achieved in 1939. The achievement meant that Pratt simultaneously held the season goalkicking record in both the Association and the Victorian Football League, in which he kicked 150 goals in 1934. Pratt's record 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.
Des Fothergill won the Association best and fairest, receiving both the V.F.A. Medal and the Recorder Cup as trophies for the achievement. Fothergill polled a huge total of 62 votes – an average of 3.1 votes per game – and was a comfortable winner ahead of E. Fay on 33 votes and Lance Collins on 32 votes. Fothergill had transferred to the Association from League club in 1941, and had shared the 1940 Brownlow Medal as best and fairest of that competition.
Williamstown won the seconds premiership. Williamstown 18.17 defeated Coburg in the Grand Final, played as a curtain raiser to the seniors Grand Final on Saturday 4 October at the Melbourne Cricket Ground.
Notable events
On 30 August, Port Melbourne 43.29 defeated Sandringham 7.9. Port Melbourne's score set a new record for the highest score in Association history, breaking Brunswick's record of 37.16 set in 1939.
Three Port Melbourne players – Ted Freyer, Austin Robertson, and R. Reynolds – were all initially suspended for the Grand Final, but successfully appealed to overturn the suspensions. In the Grand Final, Robertson and Freyer kicked twelve of Port Melbourne's fifteen goals between them.
Port Melbourne's win against Coburg in the Grand Final was the first time that Port Melbourne had defeated Coburg since July 1929.
