When the war started, he was ordered to carry a dispatch to Fort Pickens. He accomplished his mission, but on his return north he was seized by the Confederates at Montgomery, Alabama. He was imprisoned for several days. After his release, he was placed under the command of General Irvin McDowell. He participated in the First Battle of Bull Run, and gained the brevet of major for gallantry. In October he returned to New Hampshire to take command of the 7th New Hampshire Volunteer Regiment, which had been raised by Lieutenant Colonel Joseph Carter Abbott. Putnam became colonel of the regiment in December 1861. It was stationed first at Fort Jefferson, Tortugas Island, then St. Augustine, Florida, then Port Royal, South Carolina, and then around Charleston, South Carolina, South Carolina. In 1863, Putnam commanded a brigade in the Stono Inlet expedition as well as in the capture of Morris Island. He was promoted to captain in the Regular Army in March 1863. However, he had been an acting brigadier general for several months preceding the Second Battle of Fort Wagner, on July 18, 1863. In the battle, he led the 2nd Brigade, which was composed of the 7th New Hampshire, 62nd Ohio, 67th Ohio, and 100th New York. He was killed by a musket ball to the head while rallying his men. His body was not recovered.