On February 9, 1995, Desjardins was traded to the Philadelphia Flyers along with John LeClair and Gilbert Dionne in exchange for Mark Recchi and a 3rd round pick in the 1995 NHL Entry Draft (Martin Hohenberger). He was brought in to solidify the Flyers defence and that he did as he won the first of what would be seven Barry Ashbee Trophies, an award given annually to the Flyers top blueliner. He played the remainder of his career with the Flyers, achieving two NHL second team All-Star selections (1999, 2000) and two more All-Star Game appearances (1996, 2000). His 396 points with the Flyers ranks second among defencemen only to Mark Howe's 480 in team history. During the 1999–2000 season, Desjardins became the Flyers captain once Eric Lindros was stripped from captainship for his complaints about the Flyers' medical staff.