Doubleday served under General Patterson in the Shenandoah Valley, June-August 1861. He was appointed Brigadier General, United States Volunteers, February 3, 1862 and led the 2nd Brigade, 1st Division, III Corps at Second Bul Run and took command of the Division on August 30 when General Hatch was wounded. He again led the Division at South Mountain, Antietam and Fredericksburg. He was promoted to Major General, USV, November 9, 1862 and commanded 3rd Division, I Corps, at Chancellorsville, and headed that Corps when General John Reynolds was killed in the Battle of Gettysburg, July 1, 1863. On the first day, Doubleday led the Union troops in their repulse of the Confederate army until reinforcements arrived. Doubleday's top commander, Gen. George G. Meade, was not, however aware of all of the facts concerning Doubleday's meritorious service and Doubleday's division's credit for the ultimate Union victory on the third day of Gettysburg. Therefore, Doubleday did not earn the permanent command of his division; instead it was given to former West Point classmate John Newton, and Doubleday was returned to a lesser command.