Karunasekara enlisted in the Sri Lanka Army as an Officer Cadet in 1981, going on to earn his commission as a Second Lieutenant in the Sri Lanka Light Infantry after completing training at the Sri Lanka Military Academy, Diyatalawa in 1984. Over the next 35 years, he would rise through the ranks of the army, holding such key positions as Director Military Intelligence, Director Infantry, Master General of Ordnance Branch, and Military Secretary. Karunasekara has held both battalion- and brigade-level commands during the Eelam War, and has commanded the 53 Division during its course. In addition, he was appointed the commander of the Sri Lankan contingent of the UN peacekeeping mission in Haiti (MINUSTAH) when first deployed in 2004.