In 1954 Clarke participated in an IRA raid on a British Army barracks in Omagh, County Tyrone, for which he received a ten year sentence.

When the hierarchy of the Roman Catholic Church in Ireland issued an explicit condemnation of IRA violence in January 1956, Clarke severed his connections with the IRA. He petitioned for remission of his sentence in 1958, and was released from jail on 18 December 1958 after the Governor of Northern Ireland Lord Wakehurst exercised his prerogative of mercy.