With NHL play set to resume in 2005–06, Cloutier re-signed with the Canucks to a two-year, $5 million contract on August 18, 2005. Returning to the Canucks, he was injured early in the season during a game against the Avalanche on October 29, 2005. Attempting to check Avalanche forward Andrew Brunette, Canucks defenceman Nolan Baumgartner collided with Cloutier, causing a goal and forcing Cloutier out of the game with both a concussion and whiplash. The injury caused him to miss five games. Soon after returning, Cloutier was re-injured in a game against the Mighty Ducks of Anaheim on November 20, when forward Rob Niedermayer skated into the crease and collided with Cloutier. He stayed in net to complete the game, a 3–2 win, and was on the bench the following game to backup Auld. However, after aggravating the knee in a practice on November 23, an MRI revealed a partially torn anterior cruciate ligament (ACL). Electing for reconstructive knee surgery, occurring on December 15, Cloutier missed the remainder of the season.