Elected colonel of the 1st South Carolina Infantry in 1861, Hagood participated in the attacks on Fort Sumter before he was sent north. His regiment served at the Battle of First Manassas and then returned to South Carolina. In July 1862, Hagood was promoted to brigadier general. In May 1864 he returned north during the Petersburg campaign. He participated in the Battle of Walthall's Junction and in the battles of Drewry's Bluff and Cold Harbor. His unit left the siege of Petersburg to reinforce the command at Fort Fisher, NC. He surrendered at Durham Station, NC, with the army of Gen. Joseph E. Johnston.