In December 2005, Stuart was appointed as coach of Australian national rugby league team, replacing Wayne Bennett after Australia's loss in the 2005 Tri-Nations Final to New Zealand by a scoreline of 24-0. This meant that Stuart had to stand down as coach of the New South Wales State of Origin team. Stuart enjoyed success with the Kangaroos: winning the Anzac Tests of 2006 and 2007, as well as the 2006 Tri-Nations. In addition, at the end of the 2007 season, the team won a one-off Test against New Zealand.