During the First Battle of Bull Run, Smith served on the staff of Brig. Gen. Irvin McDowell. On August 13, 1861, he was appointed a brigadier general in the Union Army after helping organize the 1st Vermont Brigade. He was appointed a brevet lieutenant colonel in the regular army for his gallantry at the Battle of White Oak Swamp in the Seven Days Battles. On July 4, 1862, he received promotion to the rank of major general in the Union Army. Smith led his division with conspicuous valor during the Battle of Antietam, and was again brevetted in the regular army. When his corps commander, Maj. Gen. William B. Franklin, was reassigned to a superior command, Smith was placed at the head of the VI Corps of the Army of the Potomac, which he led at the disastrous Battle of Fredericksburg.