Hedberg signed a two-year contract with Atlanta in July 2006 and served as the backup for starter Kari Lehtonen during the first year of that contract. However, a long-term injury hindered Lehtonen during the 2007–08 season and Hedberg took over as Atlanta's starting goaltender for much of the season. On 16 June 2008, Hedberg signed a multi-year contract extension with the Thrashers. During the 2009–10 season, he shared time with Ondrej Pavelec as the primary starter after Lehtonen missed most of the season and was then traded. Despite Hedberg's good performance he and the Thrashers parted ways after the season.