When the Civil War broke out in 1861, Baird was promoted to brevet captain. He fought at the First Battle of Bull Run under Brig. Gen. Daniel Tyler. On November 12, 1861, Baird was promoted to major in the Regular Army while serving as an assistant inspector general. He became chief of staff to Maj. Gen. Erasmus D. Keyes during the first part of the Siege of Yorktown, where his service earned him a further promotion to brigadier general of U.S. Volunteers on April 30, 1862, to rank from April 28, 1862.