[3] When the Civil War broke out, he served with his regiment, rising from Private to Quartermaster Sergeant by October 1863, when he was commissioned as a Second Lieutenant.

He was promoted to First Lieutenant in April 1864[1] and later received the Medal of Honor for dragging a wounded Union officer to the rear and preventing him from being captured at the October 1864 Battle of Peebles Farm.

He was then on leave of absence from May to October, 1867; commanding a company at Fort Snelling, Minnesota to April, 1869; unassigned May, 1869; and then on duty at Galveston, Indianola, Corpus Christi, and Jefferson, Texas, until December 1869.

On February 5, 1874, detachments of Companies A and G, Eleventh Infantry, attacked a camp of hostile Qua ha dee Comanches on the Double Mountain Fork Brazos River, Texas, killed eleven Indians and captured sixty-five horses.

On June 20, 1877, About 7 o'clock Company I, Seventh Cavalry (Captain Nowlan), reached the north bank of the Yellowstone, having been detached as the escort of Colonel Sheridan, who was to proceed to the Little Bighorn for the purpose of securing the bodies of the officers who fell in the Custer fight.

Later in the day Colonel Sheridan passed up the river on the steamer Fletcher, being accompanied by Captain Schwan, Company G, Eleventh Infantry.

Captain Theodore Schwan, of the 11th Infantry, to be assistant adjutant general with the rank of major, July 6, 1886, vice Benjamin, deceased.

Two weeks before his last promotion in the regular army he was appointed brigadier-general of volunteers, and in accordance with the Act of Congress, approved March 2, 1899, he will retain that rank until July 1, 1901.

[11] That unit was exchanged with the First Division, Seventh Army Corps on June 27, and at the beginning of July, Schwan was relieved of that command by the War Department, freeing him for service with the Puerto Rican invasion.

[citation needed] With the fighting on Puerto Rico over, General Schwan was transferred to the Philippines, where he became chief-of-staff of the Eighth Army Corps, which had become engaged in the Philippine–American War.