In 1857, he enlisted as a private in Company K of the 7th Regiment of the New York National Guard, and was attached to the staff of Brig. Gen. William Hall. At the start of the American Civil War, Pierson helped organize the 1st New York Volunteer Infantry Regiment, and was appointed captain in May 1861. He was promoted several times and assumed command of the regiment on October 9, 1862, with the rank of colonel. Attached to the 3rd Corps, Army of the Potomac, he led the 1st New York in actions at the Seven Days Battles, Second Manassas and the Battle of Fredericksburg. After the Battle of Chancellorsville in May 1863, Colonel Pierson was honorably discharged and mustered out on May 25, 1863. For distinguished service, he was brevetted brigadier general of the United States Volunteers for "gallant and meritorious services."