He joined the Ballymacelligott company of the Irish Volunteers in 1914 and was involved in an abortive attempt by Roger Casement to land arms for the Easter Rising at Banna Strand in Kerry. After the rebellion he was interneed by the British at Frongoch in Wales for his role in the events. In April 1918, he led an arms raid on Gortalea Royal Irish Constabulary barracks in which two Volunteers were killed. It was one of the first acts of guerrilla warfare in the period.
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.
According to historian T. Ryle Dwyer,
"McEllistrim arguably played as important a role in the War of Independence as Tom Barry or Dan Breen but he never wrote a book about his exploits, nor was he prepared to talk about them publicly... Even though McEllistrim sat in the Dáil for over forty years, he apparently never mentioned the period in Leinster House".He rejected the Anglo-Irish Treaty and fought in the Anti-Treaty IRA during the Irish Civil War of 1922–23. He was one of the senior IRA figures in Kerry during this conflict, under the command of Humphrey Murphy. In the war's early months, he commanded a Kerry column in the fighting in Limerick city and at the Battle of Kilmallock, before retreating back into Kerry and pursuing guerrilla warfare. In January 1923, he, along with John Joe Sheehy, led an attack on the National Army barracks at Castlemaine, using an improvised mortar.
McEllistrim was elected to the Dáil as TD for Kerry in August 1923, only months after the end of the civil war, as a republican candidate. He came third in the county with 7,277 votes. He remained a Teachta Dála (TD) for the Kerry constituency, and later of Kerry North from 1926–69. After 1926 he followed much the republican leadership into Fianna Fáil. His son, Tom McEllistrim, and his grandson, also Tom McEllistrim have both represented the Kerry North constituency.