Berube, 49, became the team’s head coach in October 2013, when the team fired Peter Laviolette.
During his two seasons behind the bench, Berube led the Flyers to a 75-61-28 record with one playoff appearance, a first round loss in 2014.
This season Philadelphia went 33-31-18 and finished in sixth place in the Metropolitan Division of the Eastern Conference, drawing the ire of owner Ed Snider.
Berube played with several NHL teams, including the Flyers, between 1986 and 2003.
He also served as an assistant on Philadelphia’s coaching staff and as head coach of team’s AHL affiliate.