On March 2, 2015, Flynn was traded by the Sabres to the Montreal Canadiens for a 2016 fifth-round draft pick. On April 15, 2015, he played in his first ever playoff game and scored the game-winning goal against the Ottawa Senators in Game 1 of the Eastern Conference Quarterfinals. Following the conclusion of the 2014–15 season, Flynn re-signed to a two-year contract extension with the Canadiens on July 1, 2015.