Barnum entered the U.S. service on May 13, 1861, as captain of Company I, 12th N.Y. Infantry, at the age of 27; and afterward in October 1861 was promoted to major of that regiment. He served with distinction with that command, including the Peninsula Campaign under Maj. Gen. George B. McClellan, until July 1, 1862, when he was dangerously wounded by gunshot through the left ilium, at Malvern Hill, Virginia. At the time, the wound was supposed to be mortal; his body was abandoned and fell into the hands of the enemy, but afterward, he returned to the Union lines, so far recovered from his injury as to accept a commission as colonel in the 149th New York, dated October 4, 1862, rank September 17, 1862, and was mustered into service with the regiment at Syracuse, New York.
Not being able to assume immediate command, he joined the regiment in the field on the eve of its departure from Fairfax Station, Virginia, January 18, 1863. He soon required further surgical operations, and on April 1, obtained leave of absence and went to Albany, New York, for treatment under Dr. March.
He next joined the regiment at Edward's Ferry, Maryland, during the Gettysburg Campaign, but was still too ill to render active service only part of the time, and at Ellis' Ford, Virginia, August 6, 1863, was compelled a second time to leave the regiment, and went to Washington, D.C., for treatment.
He again joined the regiment at Wauhatchie, Tennessee, on November 10, 1863, and received a flesh wound in the right forearm while leading the charge of his regiment at the Battle of Lookout Mountain, November 24, 1863.
On December 23, in pursuance of an order of Maj. Gen. George H. Thomas, he was detailed to convey the captured flags taken by the 149th New York and other regiments to the War Department at Washington, and also received a leave of absence for twenty days, to take effect after the performance of such duty. For this service, no recognition was given at the time, but later Col. Barnum received the Medal of Honor. While absent in the performance of this duty, Barnum received further surgical treatment, and being disabled for field duty, was placed on recruiting service for the regiment, and again joined his command at Kennesaw Mountain, Georgia, about June 26, 1864, and a few days later was wounded by a fragment of shell in the right side at Peach Tree Creek, Georgia, July 20, 1864.
On September 10, following the death of Colonel David Ireland at Atlanta, Barnum assumed command of the 3rd Brigade, which he retained for the rest of the war.
At Savannah, Georgia, Barnum led his brigade, first in Sherman's command, into the captured city, and under Brig. Gen. John W. Geary had charge of its western portion during the occupancy by General Sherman. Soon after the capture of Savannah, Barnum received the brevet rank of brigadier general of U.S. Volunteers, and afterwards at Washington, D.C., the full rank of that grade to date May 31, 1865, and soon afterward the brevet rank of major general of U.S. Volunteers to date from March 13, 1865.