On 28 February 2014, Clancy signed for St Johnstone on a contract until the end of the 2013–14 season despite interests from Derry City. Clancy scored his first goal for the club, in a 3–3 draw against Celtic on 7 May 2014, which turns out to be his last appearance for the club. Clancy sustained a serious Achilles injury during training and needed an operation that ruled him out of the final of Scottish Cup. At the end of the 2013–14 season, Clancy was among four players to be released by St Johnstone.