Clouston's first coaching position was as an assistant coach with the Powell River Paper Kings of the British Columbia Junior Hockey League in 1994-95. He then served as general manager and head coach of the Grande Prairie Storm of the Alberta Junior Hockey League. During his tenure with the Storm, the team compiled a.627 winning percentage and he was named AJHL coach of the year in 1995-96. He joined the staff of the Kootenay Ice of the Western Hockey League in 1999 as an assistant coach. In the summer of 2002, he was elevated to the head coach position of the Ice, which he held for five years compiling a.655 winning percentage. The club's best season under his leadership was 2004–05 when the club made it to the Western Conference final. Clouston also served as a coach for Hockey Canada during his junior hockey coaching years, as assistant coach for the national under-18 2005 Junior World Cup gold medalists, and head coach for the 2006 team that also took home gold.
NHL coach
He joined the professional team coaching ranks in 2007, when he joined the Binghamton Senators of the American Hockey League. Clouston was elevated to the head coaching position with the Ottawa Senators on February 2, 2009, following the firing of Craig Hartsburg. Though initially named interim head coach in Ottawa, Clouston's early success was rewarded and the club signed him to a two-year contract extension on April 8, 2009. He was the eighth person to hold the head coach position in modern Senators' history. With Ottawa, Clouston had attempted to change the Senators' game plan to be more of an attacking one, creating turnovers and generating offense as opposed to the defence-first system which Hartsburg had attempted to utilize. Clouston coached the Senators to a somewhat successful 2009-10 season, finishing with 44 wins and 94 points and a berth in the Stanley Cup playoffs. The team ultimately lost in the first round to the Pittsburgh Penguins. A disappointing 2010-11 season saw Ottawa, beset by injuries to key players Daniel Alfredsson and Jason Spezza and erratic goaltending, languish in last place of the Eastern Conference standings for several weeks. General Manager Bryan Murray made a flurry of midseason trades and promoted many minor leaguers for tryouts. The Senators played better as the season wound down, but finished out of the playoffs. Clouston was relieved of his duties by GM Bryan Murray on April 9, 2011. On June 14, 2011, the Senators announced former Detroit Red Wings assistant coach Paul MacLean as Clouston's successor.
Return to the WHL
On August 3, 2011, Clouston was named Head Coach of the Brandon Wheat Kings, replacing Kelly McCrimmon, who stepped aside to focus on his duties as GM. On May 15, 2012, it was announced that Clouston would not return as head coach of the Wheat Kings. From June 1, 2013 to October 31, 2014, Clouston served as head coach of the Prince Albert Raiders. His record as the Raiders' coach was 41-41-3-2.
Coach in Germany
On January 21, 2016 Clouston was named head coach of Kölner Haie in the German DEL. He signed a deal for the remainder of the 2015-16 season, replacing Niklas Sundblad and led the Haie squad to a playoff semifinal appearance. In April 2016, he signed a new deal with Kölner Haie for the 2016-17 season. On January 19, 2017, he had his contract extended until 2019. After a series of bad results, he was sacked on November 20, 2017.
