During the final year of his contract in the 2013–14 season, MacDonald was traded by the Islanders to the Philadelphia Flyers in exchange for minor leaguer Matt Mangene, a second round pick in the 2015 NHL Entry Draft, and a third-round pick in the 2014 NHL Entry Draft on March 4, 2014. The Flyers signed MacDonald to a six-year, $30 million contract extension on April 15. On October 5, 2015, the Flyers put MacDonald on waivers. On October 6, 2015, MacDonald cleared waivers and was assigned to the Flyers' AHL affiliate team, the Lehigh Valley Phantoms.