Kelliher enlisted in the Second Australian Imperial Force on 21 February 1941, and was sent to the Middle East. He was assigned to the 2/25th Battalion, which was on garrison duty in Syria. The battalion returned to Australia in March 1942 and was sent to New Guinea, where it took part in the Battle of Buna–Gona later that year. During this battle Kelliher was arrested after allegedly running from the front. He was later court martialled for cowardice in the face of the enemy where he claimed his platoon commander had sent him back for information. The commander had been killed in the battle and Kelliher had no witnesses to his version. He was convicted, but the charge was soon after quashed and, after rejoining his unit, Kelliher stated he would prove he was no coward.