After losing the governor's race by 124 votes to Francis Lubbock, Clark became a colonel in the Texas militia during the American Civil War. In 1863 he joined the Confederate States Army and was commissioned colonel of the 14th Texas Infantry Regiment. He commanded the unit, as part of the Greyhound Division, until being wounded in the Battle of Pleasant Hill. A promotion to Brigadier General wasn´t confirmed by the Confederate Congress and he left the service; however in 1865 he was made a Brigadier in the militia. He fled briefly to Mexico at the end of the American Civil War, and returned home to Marshall, Texas.