 In November 1862, he was appointed brigadier general of Volunteers, and he assumed command of the 2nd Vermont Brigade on December 7, replacing Colonel Asa P. Blunt.Stoughton's brother, Charles B. Stoughton, assumed command of the 4th Vermont Infantry in his stead.Stoughton's appointment was never confirmed by the U.S. Senate and it expired March 4, 1863, less than a week before Mosby's Fairfax Court House Raid.