In June 1861, Pemberton entered into the Confederate army at a brigadier general. He advanced to the rank of major general, when he became the commander of the Department of South Carolina, Georgia and Florida. In October 1862, he was transferred to command of the Department of Mississippi, Tennessee, and East Louisiana with another promotion - to the rank of lieutenant general. In the siege of Vicksburg, he was forced to surrender the city on July 4, 1863. He resigned his commission of lieutenant general less than a year later in 1864. He rejoined the army as a lieutenant colonel of artillery, in which position, he served until the end of the war.