In December 1861, Warner joined the volunteer army as major of the 76th Ohio Infantry. He served in several battles in the Western Theater, including the Battle of Fort Donelson, the Siege of Corinth, and the Vicksburg Campaign. In 1863 he became lieutenant colonel of the regiment, which he led from Vicksburg to Chattanooga. He served on the staff of William T. Sherman during the Atlanta Campaign as the inspector general.