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. On recovering, he was given a division in the Army of the Shenandoah on the request of Major General Winfield Scott Hancock. On December 12, 1864, President Abraham Lincoln nominated Egan for appointment to the brevet grade of major general of volunteers to rank from October 27, 1864 for his service at the Battle of Boydton Plank Road, and the U.S. Senate confirmed the nomination on February 14, 1865.