In 1861, Gillmore was appointed the chief engineer of the Port Royal expedition. In April 1862, he was promoted to brigadier general following his successful bombardment of Fort Pulaski. In July 1863, he was promoted to major general, in command of the Department of the South. In May 1864, his corps was transferred to the Army of the James, serving as reinforcements in the siege of Petersburg, Virginia. After being injured falling from his horse, he returned to command of the Department of the South until the end of the war.