Regehr struggled in 2001–02, finishing with a team worst −24 plus/minus while occasionally being left out of the lineup as a healthy scratch. Unhappy with his season, he focused on improving his game. He overcame rib, abdominal and wrist injuries in 2002–03 to establish himself as a top defender with the team and earned a second Masterton Trophy nomination for his dedication. The Flames rewarded him with a five-year contract extension prior to the 2003–04 season. They also named him an alternate captain, a position he continuously held for the remainder of his stay in Calgary.