Hardee resigned his U.S. Army commission on January 31, 1861, after his home state of Georgia seceded from the Union. He joined the Confederate States Army as a colonel on March 7 and was given command of Forts Morgan and Gaines in Alabama. He was subsequently promoted to brigadier general (June 17) and major general (October 7). By October 10, 1862, he was one of the first Confederate lieutenant generals. His initial assignment as a general was to organize a brigade of Arkansas regiments and he impressed his men and fellow officers by solving difficult supply problems and for the thorough training he gave his brigade. He received his nickname, "Old Reliable", while with this command. Hardee operated in Arkansas until he was called to join General Albert Sidney Johnston's Army of Central Kentucky as a corps commander. Johnston would withdraw from Kentucky and Tennessee, into Mississippi, before launching a surprise attack at the Battle of Shiloh in the spring of 1862. Hardee was wounded in the arm on April 6, 1862, during the first day of the battle. Johnston was killed at Shiloh and Hardee's corps joined General Braxton Bragg's Army of Tennessee prior to the Siege of Corinth, Mississippi, until Department Commander P.G.T. Beauregard evacuated the town and withdrew to Tupelo. Beauregard was replaced by Bragg, who subsequently moved his army to Chattanooga before embarking on his Confederate Heartland Offensive into Kentucky. That campaign concluded with the Battle of Perryville in October 1862, where Hardee commanded the Left Wing of Bragg's army.