Since taking over the post in 2006, Holmgren has built the Flyers into an Eastern Conference powerhouse that reached the Stanley Cup finals last season before losing to the Chicago Blackhawks.
This season the Flyers have continued their strong play and lead the East standings.
"I'm particularly proud of the job Paul Holmgren has done with our hockey club and excited to offer him this three-year extension," Flyers chairman Ed Snider said in a statement.
"He continuously finds the right opportunities to improve our team and get us closer to our ultimate goal of winning the Stanley Cup."
(Writing by Steve Keating; Editing by Frank Pingue)