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 in September, 1862. When his brother was promoted to Brigadier General and assumed command of a brigade in November, 1862, Charles Stoughton took command of the regiment and was promoted to Colonel.