[4] 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.

[15] 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.

[16] 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.

[17] 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.

[21] Clarke joined Coventry City on 1 January 2017 as one of three new signings made by new Sky Blues manager Russell Slade, who had previously been his boss at Leyton Orient.

[25][26] On 23 June 2017, Clarke signed a one-year contract with League Two side Grimsby Town on a free transfer.

[30] He was made caretaker manager alongside Steve Nichol following the resignation of Jamie Fullarton on 15 July 2019.