Clarkson joined Bristol Rovers on 27 July 2012 having spent pre-season on trial with the club. The move reunited him with his old manager at Motherwell, Mark McGhee. He made his debut on 14 August 2012, in a 3–1 defeat against Ipswich Town in the League Cup, playing the full 90 minutes. He scored his first goal for the club in a 2–2 home draw on 8 September against Aldershot. Clarkson added more goals to his tally during the season, in a 2–1 win away at Exeter City, a 1–1 draw against Burton Albion at the Pirelli Stadium, a 2–1 home defeat against Sheffield United in the FA Cup, a 3–2 loss at home to Southend United, a 2–1 loss away at Rochdale, and another 2–2 draw at Aldershot Town on 26 December 2012.