Hütter is the former assistant coach and head coach of Red Bull Salzburg Juniors. He finished with a record of 13 wins, seven draws, and 15 losses at the club. Then he was head coach of Rheindorf Altach between 1 July 2009 and 5 April 2012. In the 2009–10 season, Rheindorf Altach lost to FC Pasching in the first round of the Austrian Cup and finished third in the league. In the 2010–11 season, Rheindorf Altach got to the Round of 16 of the Austrian Cup and finished second in the league. In the 2011–12 season, Rheindorf Altach were eliminated from the Austrian Cup in the first round. On 1 July 2012 he became manager of SV Grödig. In the 2012–13 season, Grödig were eliminated in the second round of the Austrian Cup. In the 2013–14 season, Grödig were eliminated in the first round of the Austrian Cup. They got a 2014–15 UEFA Europa League place after 3–3 draw on the final matchday against Wacker Innsbruck. Then he took over Red Bull Salzburg for the 2014–15 season His first training session was on 16 June 2014. His first match was a 10–1 win against 1. SC Sollenau on 12 July 2014. After one season he resigned on 15 June 2015. He won the double in his only season. His final match was a 2–0 win in the Austrian Cup final on 3 June 2015.