Lowell entered the Union Army in June 1861, and was commissioned as a captain in the 3rd U.S. Cavalry, transferring to the 6th U.S. Cavalry in August. He served as an aide-de-camp to General George B. McClellan during the formation of the Army of the Potomacin the summer and fall of 1861 and continued at McClellan's side during the 1862 Peninsula Campaign and the Battle of Antietam. In 1863 Lowell recruited and organized the 2nd Massachusetts Cavalry, and on May 10 was appointed its colonel. During the winter of 1863–1864, he was in charge of the outer defenses of Washington, D.C., and was engaged in repelling the raid by Confederate Lt. Gen. Jubal Early that reached the outskirts of the capital. During the Valley Campaigns of 1864, Lowell commanded a brigade of cavalry in Brig. Gen. Wesley Merritt's division of the Cavalry Corps of Maj. Gen. Philip Sheridan's army. He distinguished himself at Third Winchester and took a leading role in the Confederate rout at Tom's Brook. He was mortally wounded during the Union counterattack at the Battle of Cedar Creek on October 19, 1864. General Sheridan interceded to ensure that he was promoted to brigadier general on that day. He died on the next day at Middletown, Virginia, at the age of 29. He is buried in the Mount Auburn Cemetery, Cambridge, Massachusetts. Lowell was nominated as a brigadier general two days after his death. Since he was unable to sign his new commission after his death, Secretary of War Edwin M. Stanton authorized an exception allowing the posthumous promotion to become official. Upon hearing of his death, General George Armstrong Custer wept and Sheridan remarked "I do not think there was a quality which I could have added to Lowell. He was the perfection of a man and a soldier." In October 1863, Lowell married businesswoman Josephine Shaw, a sister of his close friend and fellow Union Army casualty Colonel Robert Gould Shaw. Her home when she was married was on Staten Island, and she became deeply interested in the social problems of New York City. She was a member of the State Charities Aid Society, and from 1876 to 1889 was a member of the New York State Board of Charities, being the first woman appointed to that board. She founded the Charity Organization Society of New York City in 1882, and wrote Public Relief and Private Charity and Industrial Arbitration and Conciliation. They had one daughter, Carlotta Russell Lowell. Lowell's first biography was written in 1907 by Edward Waldo Emerson, son of Ralph Waldo Emerson.
