Box Hill North , which was set to compete in
Division 3 of the men's competition, went into recess five days before the start of the 2026 season. In a statement, the club said it had "clearly and consistently communicated" to the VAFA that it could not field a senior team and had requested a transfer to the Thirds competition. The club denied that its withdrawal was related to its post-season celebrations, when one player wore
full-body blackface and others dressed up in costumes related to the
St Kilda schoolgirl scandal. All four players involved were suspended for up to three matches, while the club's leadership group was stood down until completing "appropriate education sessions".
St John's After 34 years in the VAFA, moved to the
Southern Football Netball League (SFNL) following the conclusion of the
2025 season. The club said the move was motivated by its location and proximity to other SFNL teams. This meant only one team was relegated from
Division 2 Men's, with going down and staying up. This was the first time a VAFA team had transferred to the SFNL since
St Francis Xavier and
South Mornington both moved at the end of the
2019 season.
Other withdrawals St Bedes/Mentone Tigers (SBMT) withdrew its women's team because of insufficient player numbers. The side had finished fifth in
Premier B Women's in 2025, where SBMT player Maddi Wilson had won the division's best and fairest award. Three
Division 3 Men's clubs – , and – chose to move into the Thirds competition. ==Premier Men's==