During the Civil War that followed he supported the treaty and joined the National Army. He was promoted to the rank of Sergeant and served as a Lewis gunner. On the morning of 28 June 1922 he reported for duty at 6 a.m. for what would turn into a week of street battles known as the Battle of Dublin. That day, during a break in the battle, he made his way to the nearby Pro-Cathedral where he married his fiancé Mary Douglas and then returned to the fight.
On 3 July Kennedy was shot through the right lung at the Provincial Bank on O’Connell Street and was brought to Jervis Street Hospital where he died of his wounds five days later. His military funeral came to Glasnevin with the coffin draped in the tricolor and followed by members of the National Army. He was laid to rest in KD 81 South, part of the army plot where Michael Collins would be buried just over a month later. Mary never married again and retained the Kennedy name, she is also buried in Glasnevin Cemetery.