At the outbreak of the war, Augur was commissioned as a major in the 13th U.S. Infantry. On his promotion of brigadier general, he received a command in the Army of the Potomac in November 1861. He commanded a division at Cedar Mountain where he was wounded. However, he quickly returned to service with a promotion to major general. He served at the siege of Port Hudson, then sent east to command the defense of Washington, until 1866 when he mustered out of service.