David Gallop says the A-League's move to independence prompted his decision to quit as Football Federation Australia's chief executive.
Gallop will stand down from his FFA job at the end of December.
He has held the role since August 2012 after a 10-year stint at the NRL's chief executive.
Gallop's decision comes just over a week after the FFA agreed to effectively cede control of the A-League to clubs in a new governance model also taking in the W-League and youth league.
He says the fresh governance model will bring fundamental changes to the management of the competitions and also the FFA.
"The (FFA) chief executive's role as it currently exists will be a very different, narrower role," Gallop said in a statement on Thursday.
"It makes sense for everyone to have time to openly determine what that new role and new leadership looks like.
"My aim is to ensure there is a seamless transition, with minimal interruption to the good work of the very many people ... who work so hard to deliver on the game's extensive agenda.
"There is plenty of work to be done including the finalisation of our bid to host the FIFA Women's World Cup in 2023.
"It would be fantastic on so many levels if Australia could secure such a huge football tournament and world event."
Gallop endured recent criticism for FFA's handling of the sacking of Alen Stajcic as Matildas coach, five months before Australia's failed campaign in France last month.
But Gallop, in his statement, said it had been "very satisfying to be part of so many important moments" in Australian soccer.
Achievements included introducing the FFA Cup, Australia's men winning the Asian Cup in 2015, and the nation's participation in men's and women's World Cups.
Gallop also cited striking a six-year media rights deal with Fox Sports for the A-League, expanding the domestic league, and strengthening women's soccer's finances as highlights of his tenure.
"There are challenges given the expectations that are created by the global mirror that is held up to the game in this country's competitive sporting landscape, but enormous growth opportunities are available if the stakeholders are united," he said.
FFA chairman Chris Nikou praised Gallop's contribution.
"David has provided strong and distinguished leadership over a long period," Nikou said in a statement.
"And particularly through a difficult last few years for FFA as we have managed the governance and structural changes around the game.
"Working together for the next six months, we will continue to reposition FFA for ongoing success."