On November 3, 1861, Smith resigned his volunteer commission as colonel in the Second California Cavalry to become chief of cavalry, in which capacity he served at the evacuation of Corinth. In 1862, he was promoted to brigadier general, then, in 1864, to major general. Smith commanded forces at Chickasaw Bluffs, Arkansas Post, Vicksburg, Tupelo, and Nashville. He also commanded the XVI Corps in the Mobile campaign, and during the Red River Campaign of 1864. Smith remained in the army after the end of the war. He resigned his commission in 1869.