Nowak, 47, was named Philadelphia Union's first ever coach and manager on May 29, 2009.
Nowak led the team to its first ever playoff appearance in 2011.
But this season has been a different story.
The team's record this season is at two wins, seven losses, and two draws, the second worst record in the Eastern Conference.
In 75 MLS games, Nowak posted a 21-30-24 record.
Union Coach John Hackworth will take over as Interim Team Manager effective immediately.
Hackworth, 42, has filled in for Nowak as head coach on multiple occasions during the club's existence.
Hackworth's first game as Team Manager will be this Saturday, June 16 when the Union host D.C. United at PPL Park at 7:00 p.m.
The news comes exactly a week after fan favorite Danny Mwanga was traded to the Portland Timbers for forward Jorge Perlaza.