Doubleday next spent time in New York City before receiving a promotion to the rank of major. After a period commanding artillery defenses around Washington, D.C., Doubleday was promoted to brigadier general of volunteers in February 1862 and placed in command of a brigade under General Irvin McDowell.
Doubleday’s first combat experience came in August 1862 at the Second Battle of Bull Run (Manassas). During early fighting near Brawner’s Farm, Doubleday dispatched nearly 1,000 of his men to support forces under General John Gibbon. His reinforcements helped temporarily hold the Union line against a barrage by General Thomas “Stonewall” Jackson’s Confederates. His unit returned to action the next day but was pushed back by forces commanded by General James Longstreet. Doubleday then led rearguard operations during the Union retreat from the field.
Reassigned to the I Corps under General Joseph Hooker, Doubleday next participated in the Battle of South Mountain in September 1862. After General John P. Hatch was wounded in the fighting, Doubleday took command of his division and successfully withstood a Confederate assault. He remained in division command for the Battle of Antietam, in which his unit sustained heavy casualties at an area known as “the Cornfield.” For his performance at Antietam, Doubleday was promoted to major general of volunteers in November 1862.
Doubleday’s force was lightly engaged at the Battle of Fredericksburg in December 1862, and he was placed in charge of the newly created Third Division a month later. Doubleday commanded his new unit at the Battle of Chancellorsville in May 1863 but was kept in reserve during the Union defeat.
Doubleday would play a significant role in the Battle of Gettysburg in July 1863. During the first day of fighting, he was forced to take command of the I Corps following the death of General John Reynolds. Choosing to follow through on the battle plan already enacted by Reynolds, Doubleday ordered his men to hold positions near the Chambersburg Pike. His stubborn defenses finally collapsed in the late afternoon, and his I Corps then retreated through the town of Gettysburg to the heights at Cemetery Hill.
Despite having fended off a superior force of Confederates for several hours, Doubleday was relieved of command of the I Corps by General George Meade. He participated in the second and third days of the battle as a division commander, and was wounded in the neck by a shell fragment in the aftermath of Pickett’s Charge.