Appointed as chief engineer of the Department of the Ohio, he served in western Virginia in 1861. He served on the field in the advance on Corrick's Ford, WV, and received a commission as a brigadier general. He was not suited for a field command, so he was reassigned after his failure at Secessionville, South Carolina, in June 1862. His commission was revoked in August 1862. For the rest of the war, Benham served as commander of the engineer brigade of the Army of the Potomac.