On March 30, 2000, Sandelin accepted the job as the head coach of the University of Minneasota-Duluth Bulldogs for long time Bulldog coach Mike Sertich. As head coach he has led the Bulldogs to six 22+ win seasons, eight NCAA tournament appearances in (2003–04, 2008–09, 2010–2012, 2015–2019). In (2008–09) he knocked off his former North Dakota team to become the WCHA Final Five Champions. Then in (2010–2011) the Bulldogs made a run in the NCAA tournament to become the 2011 NCAA Champions, beating Yale, Union, Notre Dame and Michigan for the title. . He made the Bulldogs the second Division I collegiate team in Minnesota to take home the Frozen Four Title, the Minnesota Golden Gophers (5) and the Bulldogs (3). In (2003–04) he was named the WCHA Coach of the year and the National Coach of the year posting a 28–13–4 record and leading the Bulldogs to a third-place finish in the Frozen Four. He has also produced two Hobey Baker winners in Junior Lessard in 2004 and Jack Connolly in 2012, along with 15 future NHL hockey players and 17 All WCHA selections. During the stretch he was the US National Junior coach in 2005 and assistant coach in 2012. In the 2011–12 season he led the Bulldogs to a 17-game unbeaten streak, and the first time in Bulldog history at the number one in the USCHO polls for 9 straight weeks. In 2016, he signed a 4-year extension, keeping him under contract until the 2020–2021 season.