Football Federation of Australia chief executive David Gallop announced Thursday he will retire at the end of the year as the governing body restructures to give clubs more say in running the game.
Gallop, who has held the top job in Australian football for seven years, linked his decision to the planned shake-up which will see the chief executive's role diminished.
A working group charged with reviewing the structure of Australia's professional leagues announced a host of recommendations last week that will see clubs take greater control of the elite competitions.
Under the proposal a new organisation, made up largely of representation from each of the clubs, will govern the A-League, women's league and youth leagues as they transition away from FFA control.
Gallop said in a statement that the recommendations would bring about "fundamental changes" to the way the way professional competitions are managed, making the FFA chief executive's role "narrower".
"It makes sense for everyone to have time to openly determine what that new role and new leadership looks like," he added.
"Football is the true world game and many Australians from all backgrounds want to see it grow bigger and stronger in the decades to come."
Gallop and the FFA came under intense pressure this year following the controversial sacking of women's coach Alen Stajcic in January just months before the World Cup.
The FFA dismissed Stajcic citing concerns over unspecified "workplace" and "player welfare" issues following two confidential surveys about the team environment and culture, as well as interviews and other information.
Authorities were forced to make an embarrassing apology to Stajcic in May after months of innuendo and speculation after the FFA provided no concrete details for the surprise move.
FFA Chairman Chris Nikou said Gallop's decision was "predicated" on the future changes for professional governance.
"David has provided strong and distinguished leadership over a long period and particularly through a difficult last few years for FFA as we have managed the governance and structural changes around the game," Nikou said.