Karunakaran was born on 1 October 1963. He was educated at Cheddipalayam Maha Vidyalayam and St. Michael's College, Batticaloa. Following the Black July anti-Tamil riots he left school in August 1983 and in November 1983 he joined Tamil Eelam Liberation Organization (TELO), a Tamil militant group. He received Guerrilla warfare training and June 1987 became TELO's regional leader in Ampara District and Batticaloa District. Later he became general-secretary of TELO.