Leaving Minnesota, Clarke returned to Philadelphia to assume the role of Senior Vice President during the 1992–93 season, and served as a mentor for young phenom Eric Lindros during his first season. Clarke moved on shortly after and took the general manager position with the expansion Florida Panthers, a team that set the expansion team record for wins and points during a season in 1993–94. He returned to the role of Flyers general manager prior to the 1994–95 season (Florida was compensated with cash and Philadelphia's second-round draft pick in the 1994 NHL Entry Draft), and he rebuilt the team into a Cup contender. During his second tenure as general manager of the Flyers, the team made the playoffs 11 seasons in a row but reached the Finals once (1997). Following a poor start to the 2006–07 season, Clarke resigned citing a possible burnout and a lack of desire. Clarke returned to the franchise on December 4, 2006, and was named Senior Vice President.