During the American Civil War Norton served with distinction in the Union Army as a quartermaster in a New York Regiment, then as a lieutenant colonel in the 5th Army Corps, Army of the Potomac, on the staff of General Fitz John Porter, headquartered at Harrison's Landing on the James River in Virginia. and was present at the Second Battle of Bull Run in Virginia, and at the Battle of Antietam in Maryland in 1862. He was brevetted brigadier-general in 1863, after which he resigned his commission on January 6 of that year.