In 1861, Fagan recruited the 1st Arkansas Infantry, of which he was soon elected colonel. He led them into action at the Battle of Shiloh, which earned him a promotion to brigadier general. He soon transferred to the Trans-Mississippi Department where he participated in the Battle of Prairie Grove, the Camden expedition, and the invasion of Missouri. He also commanded troops at the Battles of Marais des Cygnes and Mine Creek. In April 1864 he received his second promotion--to major general. He was captured in late 1864. He was not paroled until June 1865.