[1] Following the outbreak of the Civil War, Fessenden received a commission as a captain in the Regular Army in the newly raised 19th U.S. Infantry on May 14, 1861.

[2] In January 1862, he assumed duties as a line officer in the Army of the Cumberland in Tennessee and was severely wounded at the April 1862 Battle of Shiloh.

He became the colonel of the 25th Maine Infantry and commanded a brigade as part of the 22nd Army Corps in the defenses of Washington, D.C.

[2] On May 10, 1864, he was promoted to the rank of brigadier general and served later that year in command of a brigade in the army of Nathaniel P. Banks in the Red River Campaign.

After convalescing, he was assigned to administrative duty for the rest of the war, commanding various garrisons and supply trains.

He served on the military commission that oversaw the war crimes trial of Henry Wirz, who was executed for his controversial actions while commanding the Andersonville Prison in Georgia.

He was promoted to major general of volunteers on November 19, 1865, and assigned command of the 1st Division of the Department of West Virginia.