The former Liverpool striker has agreed to a two-year contract and will take charge of the Australian team from the start of the 2019 season.
The 44-year-old has previously played in the league for North Queensland Fury and Perth Glory between 2009 and 2011 and said he was happy to be returning Down Under.
Fowler's playing career ended in 2012 and his only previous managerial experience came during a short spell with Thai side Muangthong United in 2011-12.
Over the past seven years Fowler has been coaching at Liverpool's academy programme.
"I have worked really hard getting all my badges, so to just quash all the inexperience rumours, I'm experienced in terms of getting all my coaching hours in and this is where I want to be," said Fowler.
"I've been in football a long time. Obviously, this is my first big, big role and one I'm really looking forward to. I'm really excited."
The team currently sit second from bottom in the table, with only four wins from 26 matches, but Fowler said he was confident of being able to turn around the club's fortunes.
"It's unfortunate for a club the size of Brisbane to be having a tough time but I'm all for looking for the positives.
"I was a player who was passionate, committed, I had that drive and I want to bring that type of player to Brisbane Roar.
"It's a tough job, it's a tough ask, but I believe I'm the right man to do that, bringing in the right player.
"Brisbane have had some fantastic years in terms of what they've won. The way they played football was really, really good, very easy on the eye, so of course I want to do that and I think a club the size of Brisbane deserve to be back at the top levels of Australian football - and we will be there."
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