He was commissioned adjutant of the 4th Vermont Infantry on August 1, 1861, and mustered into military service on September 21 under the command of his brother, Col. Edwin H. Stoughton. He was promoted to major on February 25, 1862. He was present in action at all the regiment's battles during the Peninsula Campaign.
Stoughton was promoted to lieutenant colonel on July 17, 1862, and saw action at Crampton's Gap, where the regiment captured 121 men and the colors of the 15th Virginia Infantry. He subsequently served at Antietam. He assumed command of the regiment with his promotion to colonel on November 5, 1862, when his brother was promoted to brigadier general of volunteers.
Stoughton first led his regiment at the Battle of Fredericksburg, on December 13, 1862, where 4th Vermont suffered 56 casualties. Stoughton reported "My colors were completely riddled with canister and musket balls, scarcely hanging together. The top of the staff, upon which is a brass eagle, was shot away by canister, but saved, and brought away."
Colonel Stoughton continued to lead his regiment in the battles of Marye's Heights, Salem Church, and Gettysburg. On July 10, 1863, during the Union army's pursuit of the retreating Army of Northern Virginia, Stoughton was severely wounded in an engagement near Funkstown, Maryland, resulting in the loss of his right eye. He resigned from the army on February 2, 1864, as a result of his wounds. In the omnibus promotions that followed the end of the war, he was brevetted Brigadier General, Volunteers, for faithful and meritorious services, dating from March 13, 1865.
He died in Bellows Falls, Vermont, and is buried in Immanuel Cemetery in that town. His widow, several years after his death, applied for a widow's pension from Connecticut.
Charles Stoughton and his wife Ada Ripley (Hooper) Stoughton, were the grandparents of Dr. Benjamin McLane Spock, 1903–1998, a leading pediatrician and peace advocate.
- The Genealogy Page
- Report of Charles B. Stoughton to Peter T. Washburn, December 16, 1862, Report of the Adjutant & Inspector General of the State of Vermont, from November 1, 1862, to October 1, 1863, Montpelier: Walton's Steam Printing Establishment, 1863, p. 73.
- General Index to Pension Files, 1861-1934. Washington, D.C.: National Archives and Records Administration. T288, 544 rolls.
- Notable Descendants of Henry and Margaret Howland
- Benedict, G. G., Vermont in the Civil War. A History of the part taken by the Vermont Soldiers And Sailors in the War For The Union, 1861-5. Burlington, VT.: The Free Press Association, 1888, i:158, 161, 163-164, 166-167, 353, 394, 414.
- Crockett, Walter Hill, Vermont The Green Mountain State, New York: The Century History Company, Inc., 1921, pp. 541, 575.
- Peck, Theodore S., compiler, Revised Roster of Vermont Volunteers and lists of Vermonters Who Served in the Army and Navy of the United States During the War of the Rebellion, 1861–66, Montpelier, VT.: Press of the Watchman Publishing Co., 1892, pp. 108, 750-751.
- Charles B. Stoughton at Find a Grave Retrieved on 2008-11-04