Clarke is a product of the Huddersfield Town Academy. He began his first team career at the age of just 17 when his debut came in a 1–1 draw away to Stoke City on 8 September 2001. He scored his first goal for his home club on his home debut in the game in which ended in a 4–2 loss against Blackpool. He made a total of 37 starts in all competitions during the 2001–02 season his first as a professional with the first team with 36 of them coming in the league scoring once.
Clarke was runner-up in the Huddersfield Town 'Player of the Year' 2005–06 and was made vice-captain of the team aged just 21, going on to win the title the following year along with winning the 'players player award'. Clarke played under eight different managers at the Galpharm and was in the starting 11 for each one.
Clarke has been selected in FourFourTwo's Top 50 Football League Players at 43 in March 2006, down from 40 in the list in March 2005.
On 19 August 2011, he joined Oldham Athletic on a five-month loan deal. He made his debut the following day, where he also scored the first goal. Clarke returned to his parent club Huddersfield Town after making 16 appearances for Oldham. He then on 9 March, joined Bury on loan for the remainder of the season. He played a huge part in the club's league survival in the league, with them finishing mid table.
Clarke signed for Leyton Orient on 18 July 2012 on a two-year contract. Boss Russell Slade made him the club captain of the London side within a week of being signed. On 14 February 2014, he signed a contract extension at Leyton Orient. He scored his first goal for the club on 11 March 2014 in the 2–0 win at Port Vale, a header at the near post from a corner. Two games later, Clarke scored an equalising goal in the 1–1 draw at Walsall, a deflected half-volley long-range shot in the 77th minute. Clarke was part of the team that played in the 2014 Football League One play-off Final against Rotherham United, the game finishing 2–2 Orient lost 3–4 in a penalty shoot out.
Clarke joined Bradford City on 28 July 2015 on a one-year contract.
On 23 June 2017, Clarke signed a one-year contract with League Two side Grimsby Town on a free transfer. He scored his first goal for Grimsby on his debut in a 3-1 win over Chesterfield on 5 August 2017.
