Serving under Gen. Robert E. Lee, Barton saw action at the battles of Cheat Mountain and Greenbrier River, and later with Gen. Thomas "Stonewall" Jackson as chief engineer during the Valley Campaign in 1862.

Released following a prisoner exchange, Barton was assigned command of the Virginia brigade once led by Lewis Armistead, serving under Maj. Gen. George Pickett.

Barton was commanding one of the forward columns marching on New Bern, in February 1864, when he was censured after Pickett had issued a formal complaint against him for lack of cooperation.

Barton was later returned to command due to the intervention of other officers on his behalf and assigned to a brigade defending Richmond, Virginia, under Lt. Gen. Richard S. Ewell.

Imprisoned for three months at Fort Warren in Boston, Massachusetts, he was released after signing a loyalty oath to the Union After the war, Barton returned to Fredericksburg, where he began practicing chemistry, eventually becoming one of the most prominent chemists in the United States.