On 29 June 2009, Budaj was re-signed by the Avalanche to a one-year contract for the 2009–10 season. He started the season playing as the Avalanche backup goalie to Craig Anderson, formerly of the Florida Panthers. Before his first appearance in net, Budaj was diagnosed with the H1N1 virus and was completely isolated from the rest of the team until he was cleared to play by the coaching staff. Budaj finally made his first appearance of the season on 4 November, against the Phoenix Coyotes. He stopped 28 of 29 shots and backstopped the Avs to a 4–1 victory. Budaj made his second post season appearance on 22 April 2010 against the San Jose Sharks, when he relieved Craig Anderson at 11:05 in the third period. The Sharks won the game 5–0, with one goal scored against Budaj.