In 1878, at the age of 20, he joined the Irish Republican Brotherhood (IRB) following the visit to Dungannon by John Daly, and by 1880 he was centre (head) of the local IRB circle. In August that year, after a member of the Royal Irish Constabulary (RIC) had shot and killed a man during riots between the Orange Order and the Ancient Order of Hibernians in Dungannon, Clarke and other IRB members attacked some RIC men in Irish Street. They were driven back, however, and Clarke, fearing arrest, fled to the United States.