In 1862 Harding joined the U.S. Army as a private in the 83rd Illinois infantry. In August 1862 he was promoted to colonel just before his unit was appointed to garrison duty at Fort Donelson. On February 3, 1863, he commanded Union forces during an attack on the fort by Confederate forces under Forrest and Wheeler, which he successfully repelled. In March 1863, he was appointed Brigadier General of Volunteers before he resigned his command in June 1863 due to poor eyesight.
