The club released a statement on Sunday confirming the news after reports of Mulvey's axing.
"Head coach Mike Mulvey met with Brisbane Roar FC management today. As a result, he will step down from the head coach's position," Roar chief executive Simon Dobson said.
"Brisbane Roar FC thanks Mike Mulvey for his contribution to the success of the club since his appointment as interim coach in December 2012 and as Brisbane Roar head coach in February 2013."
Local media reports have claimed Dutchman Frans Thijssen - whose previous managerial positions include roles at Vitesse, Malmo, Fortuna Sittard and several stints in the Middle East - will replace Mulvey, although the club are yet to comment on who will take over on an interim basis.
Mulvey succeeded Rado Vidosic in December 2012, guiding the then-faltering champions into a finals berth, before orchestrating Roar's third title-winning campaign in four seasons last term.
The loss of star striker Besart Berisha and Australia international Ivan Franjic has been keenly felt in a start to a 2014-15 campaign that has produced just one win to date. Roar lost 1-0 away to Melbourne Victory on Friday.