In 1941, the VFL competition consisted of twelve teams of 18 on-the-field players each, plus one substitute player, known as the 19th man. A player could be substituted for any reason; however, once substituted, a player could not return to the field of play under any circumstances. Teams played each other in a home-and-away season of 18 rounds; matches 12 to 18 were the "home-and-way reverse" of matches 1 to 7. Once the 18 round home-and-away season had finished, the 1941 VFL Premiers were determined by the specific format and conventions of the Page-McIntyre System.
The seconds premiership was won by. Essendon 12.16 defeated 9.17 in the Grand Final, played as a curtain-raiser to the senior Grand Final on Saturday 27 September at the Melbourne Cricket Ground.
During March, the players of the Geelong Football Club went on strike and refused to train over a pay dispute. The players were seeking £3 per week, but the club was offering £1/10/– per week, which upset the players as they had received pay cuts in 1940 when the club had made the finals and finished the year in a strong financial position. In response, the club claimed the lower offer was due to the extra expense of moving from Corio Oval to Kardinia Park, and increased payments to war funds drove the decision. The majority of players acquiesced and accepted the £1/10/– offer, but five senior players did not. Three of those crossed to the Victorian Football Association without a clearance – Allan Everett going to Preston, Bernie Hore going to Coburg, and Alan "Nipper" Marsham to Williamstown – while the other two, George Dougherty and Tom Arklay, having trained in the pre-season with the VFA clubs Coburg and Preston, eventually returned to play with Geelong in the 1941 season.
In the Round 2 match between Carlton and Richmond, 11 players were injured, while highly talented Carlton rover Jack Hale, who broke his leg in an accidental collision with Richmond centreman Bernie Waldron, never played again.
The VFL postponed its Round 5 matches and conducted its second patriotic lightning carnival at the Melbourne Cricket Ground on Saturday 24 May 1941. Collingwood won the carnival, defeating Melbourne 3.2 to 3.1. The carnival raised £1,526 for the war effort.
In the last minutes of the last quarter of the Second Eighteens Grand Final, played at the MCG on 27 September 1941, which Essendon, captain-coached ex-Collingwood player Harry Collier, won to 9.17 ), a Fitzroy player felled an Essendon player and fights broke out all over the ground. As the final bell was sounding, a vicious bench-clearing brawl broke out involving almost every player, with many of the players felled by punches and kicks. Both teams were reported for "unseemly conduct", and following the VFL investigation committee's hearing conducted on 14 October 1941, each club was fined £10.
In a lop-sided senior Grand Final, Melbourne, missing at least twelve of its 1941 senior players through either injury or military service, was 47 points ahead at three quarter time, and went on to beat Essendon by 29 points: 19.13 to 13.20.
After defeating Collingwood in Round 5, Carlton had a winning record over every other team in the competition in combined regular season and finals matches. They would hold this distinction until Round 8 of the 1954 VFL season.