Clarkson has played most of his professional career in Scotland for Motherwell, where he played for a total of seven seasons at the beginning of his career.
Born in Bellshill, Scotland, Clarkson made his debut for local club Motherwell in December 2002, scoring his first goal nine minutes into his first starting appearance for the club, at home in an SPL match against Partick Thistle on 2 January 2003. Clarkson went on to score three goals in his first season, and was a regular from the following season, playing in the majority of matches. He scored 13 goals for Motherwell in the 2007–08 season, during which his uncle, Phil O'Donnell, collapsed and later died from heart failure during a match against Dundee United. Clarkson was later voted player of the year. Clarkson went on to wear O'Donnell's old squad number, 10, during the 2008–09 season.
On 29 June 2009, Clarkson joined Bristol City and signed a three-year contract for an undisclosed fee, reportedly £800,000. Clarkson scored on his debut for Bristol City, in a 2–2 draw at Preston North End. On 6 February 2010, he scored an equaliser for Bristol City against Coventry City, the match finished 1–1. He scored his third goal for City at home to Leicester City. On 21 August 2010, Clarkson scored his first goal in the 2010–11 season in a 3–3 draw with barnsley. He netted his second of the season in a 2–0 win over Scunthorpe United at Glanford Park, the goal in the 90th minute.
On 1 May 2012, Clarkson was released by Bristol City.
Clarkson completed a one-month loan move to Brentford on 15 September 2011 and made his debut in the away win at Oldham Athletic on 24 September. He scored his first goal for the club away to Carlisle United on 8 October 2011, in a 2–2 draw. Clarkson gave Brentford the lead within the first 10 minutes, but on 63 minutes, he scored an own goal when he stuck a leg out from a cross and unfortunately put the ball into the his own net to give Carlisle a 2–1 lead. He made amends by assisting for Toumani Diagouraga to level the match two minutes from the end.
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.
It was announced on 28 February 2013 that Clarkson would miss the rest of the season due to an ankle injury. Clarkson was one of 12 players released by Bristol Rovers in May 2014, after the club had been relegated to the Conference National. He scored 13 goals in 69 games for Bristol Rovers.
After leaving Bristol Rovers, Clarkson had a trial spell with Motherwell in July 2014, but was not offered a contract. He also played in pre-season as a trialist for Kilmarnock and St Johnstone.
On 8 September 2014, Clarkson signed for Dundee. He scored on his debut for the club, a 2–1 defeat against Ross County on 27 September 2014. Clarkson went on to score eight goals in his first eight games for the club, scoring in every match and his form was rewarded when he won the SPFL Player of the Month award for November. Clarkson left Dundee at the end of the season having not been offered a new contract.
On 25 June 2015, Clarkson signed for Motherwell for a second time, signing a one-year contract with the option of a second year. He made his second debut for the club on 1 August 2015, in a 1–0 win against Inverness Caledonian Thistle. After making only seven appearances as a substitute during the 2015–16 season, Clarkson signed on loan with Scottish Championship side St Mirren in January 2016, with the deal lasting until the end of the season.
After being released by Motherwell, Clarkson returned to Paisley signing a one-year deal with St Mirren in May 2016.
Clarkson was called up by George Burley for Scotland's friendly match against the Czech Republic on 30 May 2008. He came on as a substitute in the match, and scored Scotland's only goal in the 85th minute when he took down a cross, spun and fired past Czech keeper Petr Čech. Clarkson got his second cap coming on as a substitute, in a 1–0 friendly loss to Argentina on 19 November 2008.
Clarkson played for and captained the Scotland B team, in a 3–0 friendly win over the Northern Ireland B team on 6 May 2009.Scores and results list Scotland's goal tally first
Scottish Premier League: Third Place: 2007–08
Scottish League Cup Runner-up: 2004–05
Scottish Premier League Young Player of the Month: January 2004
SPFL Player of the Month: November 2014
As of 5 February 2017
Clarkson's uncle Phil O'Donnell played alongside him at Motherwell, before his death in 2007. He has several other family members who have been professional footballers. His cousin Stephen O'Donnell last played for Clyde and another cousin Brian Dempsie previously played for Motherwell.