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.