Holabird served as quartermaster of the Union Army encampment in Harrisburg, Pennsylvania from June to August, 1861. He was quartermaster of the camp in Frederick, Maryland from August, 1861 to July, 1862. He was quartermaster of the division commanded by Nathaniel P. Banks in July and August of 1862, followed by assignment as the quartermaster of the Army of Virginia's II Corps. Holabird took part in the Northern Virginia campaign, then served with the Army of the Potomac during the Maryland campaign, including the Battle of Antietam on September 17, 1862.