When the Civil War began, Morgan was appointed Lieutenant Colonel of the 10th Illinois Infantry Regiment on April 29, 1861. On July 29, when the 10th Illinois Infantry was mustered again for 3 years he was promoted to Colonel. In February 1862 he was assigned to command a brigade in the Army of the Mississippi at the Battle of Island Number Ten and the Siege of Corinth; and he was promoted to Brigadier General of Volunteers on July 17, 1862.