Egan joined the
40th New York Volunteer Infantry Regiment, called the Mozart Regiment, in April 1861 at the beginning of the Civil War, as a private. (The regiment was sponsored by the
Democratic Party's
Mozart Hall Committee.) Egan was made lieutenant colonel on June 14, 1861. Lieutenant Colonel Egan participated in most of the major battles of the
Army of the Potomac. Initially, the Mozart Regiment served in first division
III Corps. Col. Egan is reported to have arrested the colonel of the regiment for misconduct at the
Battle of Fair Oaks in May 1862. In June 1862, Egan was promoted to the rank of colonel. He led the regiment at the
Second Battle of Bull Run, the
Battle of Chantilly and the
Battle of Chancellorsville. At Chancellorsville, Colonel Egan became acting commander of first brigade first division III Corps, when Brigadier General
Charles K. Graham was assigned to command of the third division following the death of Major General
Amiel W. Whipple. At the
Battle of Gettysburg on July 2, 1863, Colonel Egan, once more leading his regiment, was wounded in action near
Devil's Den, being hit in a leg; and the regiment's monument stands near that site. The Mozart Regiment lost 150 of 431 troops engaged. Egan also led the Mozart Regiment in the
Bristoe Campaign during the autumn of 1863, and replaced Col.
Régis de Trobriand in command of the brigade immediately prior to the winter
Mine Run Campaign. Just before Lieutenant General
Ulysses S. Grant's
Overland Campaign of 1864, III Corps was dissolved. First division became third division
II Corps. Egan led his regiment in the
Battle of the Wilderness. He became commander of a brigade during the
Battle of Spotsylvania, after Brigadier General
J. H. Hobart Ward was relieved for drunkenness on the night of May 12, 1864. His command was involved in a counterattack against the Confederates during the fighting at Harris Farm. Egan led the brigade at the
Battle of North Anna, attacking Henagan's Redoubt. He also led it at the
Battle of Cold Harbor. Egan was wounded during the
Second Battle of Petersburg in June 1864, suffering slight paralysis as a result. Colonel Egan received his commission as brigadier general on September 3, 1864. (
Secretary of War Edwin Stanton personally handed him his commission.) At the
Battle of Boydton Plank Road on October 27, he commanded the second division II Corps in place of Brigadier General
John Gibbon. Egan was seriously wounded on November 14, 1864. The wound disabled his right arm. ==Later life==