A-League chief Damien de Bohun will quit his role at the helm at the end of the 2015-16 season due to family reasons.
De Bohun has been in the position since 2012, enduring a mixed time that has included marquee signings and club crises.
Football Federation Australia chief executive David Gallop praised De Bohun, the longest-serving head of A-League in the competition's history.
"Damien brought incredible energy and dedication to the task, which spans a huge range of sporting, business and regulatory issues," he said.
"Running the A-League is a seven day a week undertaking. Damien did that while travelling across the nation and New Zealand to be on the ground with clubs to better understand their key issues and environment.
"I totally understand his decision to return to Melbourne and wish him all the best."
Under De Bohun's watch, Brisbane Roar and the Newcastle Jets have gone through ownership worries, with the latter still in FFA hands.
A recent fan crisis was among the last times De Bohun spoke publicly and the announcement comes a day after the FFA released its four-year strategic plan.