At the outbreak of the war, Sturgis was in command of Fort Smith, Arkansas. He marched to Fort Leavenworth, Kansas. Sturgis received a promotion to major going into action at the Battle of Wilson's Creek. He was soon promoted to brigadier general, in command of the defenses of Washington. Sturgis served in the Battle of Second Manassas, and in the subsequent battles of South Mountain and Antietam. He was ordered to Tennessee, and then to Mississippi. In the operations about Dandridge, which lasted from December 1863 to January 1864, Sturgis commanded the Union forces at the battles of Mossy Creek, Dandridge, and Fair Garden. In the following year, in June 1864, Sturgis oversaw the Union forces at the Battle for Brice's Crossroads, Mississippi was mustered out in August 1865.