McEllistrim served in the Irish Republican Army in Kerry throughout the Irish War of Independence of 1919–21. He was instrumental in the setting up of first an Active service unit (in June 1920) and then a larger "flying column", or full-time guerrilla unit in the IRA's Second Kerry Brigade in early 1921. His column fought in both the Clonbanin Ambush and the Headford Ambush in the spring of 1921. At the latter action, in which the IRA ambushed a train carrying British troops, Dan Allman, the leader of the flying column was killed, leaving McEllistrim in command.