Cling man resigned from the U.S. Senate to enlist in the Confederate army. He received a commission as colonel of the 25th North Carolina Infantry. He served in North Carolina and South Carolina until early 1864 when his regiment marched to Virginia. He participated in the battles of Cold Harbor, Drewry's Bluff, and Petersburg. He was wounded during the siege of Petersburg in the Battle of Globe Tavern and did not recover until April 1865.