American Civil War Stoughton resigned his regular commission in March 1861 and in September was appointed commander of the
4th Vermont Infantry with the rank of colonel. He was only 23 at the time of his appointment and was said to be the youngest colonel in the army. He led his command in the
Peninsula Campaign, and his effective performance led to his selection for promotion and command of a brigade. 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.
Mosby's Rangers (led by Confederate officer
John S. Mosby) led a daring raid into Union Territory and captured Stoughton at
Fairfax Court House on March 9, 1863. Stoughton had hosted a party for his visiting mother and sister, who were staying at the home of Confederate spy
Antonia Ford. After leaving the party, Stoughton retired to a nearby house that served as his headquarters. Mosby allegedly found Stoughton in bed, supposedly rousing him with a slap to his rear. Upon being so rudely awakened, the general shouted, "Do you know who I am?" Mosby quickly replied, "Do you know Mosby, general?" "Yes! Have you got the rascal?" "No but he has got you!" In his own written account of Stoughton's capture, which appeared in Volume III of 1888's
Battles and Leaders of the Civil War, Mosby did not mention the supposed "spanking" incident. It is however mentioned in Mosby's
Memoirs. Allegedly, Stoughton was not popular with the officers and men of the brigade, and few mourned his loss. U.S. President Lincoln, on hearing of the capture, said that "he did not so much mind the loss of a brigadier general, for he could make another in five minutes; 'but those horses cost $125 apiece!'" Blunt resumed command and led the brigade until he turned command over to Brigadier General
George J. Stannard on April 20. Stannard led the brigade until the
Battle of Gettysburg. After a two-month stay in
Richmond's
Libby Prison, Stoughton was exchanged, but saw no further service. The
U.S. Senate had not confirmed his initial appointment, and he was not re-appointed. He resigned from the Union Army in May 1863 and moved to New York. ==Later life and death==