On July 2, 2001, Roenick signed as a free agent with the Philadelphia Flyers. In his first season with the Flyers he won both the Bobby Clarke Trophy (MVP) and Yanick Dupre Memorial (Class Guy) team awards. He led the team with 46 assists, 67 points, and a +32 plus/minus rating as the Flyers won the AtlanticDivision title.

In 2002–03, Roenick led the Flyers with 27 goals and 59 points as the team won 45 games and finished second in the Atlantic Division. He also co-led the Flyers with 32 assists and eight power-play goals.

On November 16, Roenick played in his 1,000th NHL game. In February, he played in the mid-season All-Star Game. In the playoffs, he scored eight points in 13 games as the Flyers reached the second round before losing to the Senators.

On February 12, 2004 during a game vs. the New York Rangers, Roenick was hit in the face by an errant slapshot from Rangers defensemen Boris Mironov. The force of the shot broke Roenick's jaw in 19 places and knocked him unconscious for several minutes as he lay on the ice in a pool of blood. Roenick suffered his ninth concussion on the play, and there was concern that he had suffered damage to his brain's circulatory system, in addition to the broken jaw, leading him to consider retirement.

Further testing revealed no circulatory damage and Roenick returned ahead of schedule, after missing more than a month of hockey due to the concussion and broken jaw, with less than two weeks left in the season.

In 2003–04, Roenick was limited to 62 games, but still scored 47 points as the Flyers won their third division title in five years. He finished second on the team with a .76 points-per-game average.

In the playoffs, Roenick helped the Flyers reach the Eastern Conference finals, scoring 4 goals and 13 points, including the series-clinching overtime goal in game six of the second round series against the Toronto Maple Leafs.

The Flyers lost in the Eastern Conference finals to the eventual Stanley Cup champion Tampa Bay Lightning.