 Mullen turned to coaching in 2000, joining the Penguins'staff as an assistant under Ivan Hlinka. He remained on the staff when Hlinka was fired one year later, under replacement Rick Kehoe, then Ed Olczyk. Mullen was removed from his role midway through the 2005 – 06 NHL season when the Penguins fired Olczyk and his entire staff. He was retained by the organization, however, and named interim head coach of the Wilkes-Barre / Scranton Penguins for the remainder of the American Hockey League (AHL) season. In 52 games, Mullen achieved a record of 28 wins, 16 losses, 3 ties and 5 overtime losses. The Penguins chose not to retain Mullen following the season. He moved to Pittsburgh's cross-state rival, the Philadelphia Flyers, first as an assistant with the AHL's Philadelphia Phantoms in 2006 – 07, then joining the NHL team in 2007. Mullen coaches the team's power play, and was a member of the staff when the team reached the 2010 Stanley Cup Final. He remains on the Flyers' staff for the 2012 – 13 season.
