Pemberton grew up and was educated in Philadelphia, entered West Point in 1833, and graduated four years later. He fought in the Mexican War and was cited for bravery while participating in many of the crucial battles of 1846 and 1847.

Upon the outbreak of the American Civil War, Pemberton resigned his commission on April 24, 1861, and went to Richmond to offer his services to the Confederacy. Made a lieutenant colonel on April 28, 1861, Pemberton began organizing the cavalry and artillery in Virginia. On May 8 he was promoted to colonel and on June 17 to brigadier general; on Feb. 13, 1862, he became a major general in command of South Carolina, Georgia, and Florida. In October 1862 Pemberton was made lieutenant general and given command over Mississippi, Tennessee, and eastern Louisiana.

Ordered by President Jefferson Davis to hold Vicksburg at all costs, Pemberton conducted a stubborn defense despite his lack of adequate food, ammunition, and manpower. General Ulysses S. Grant (Grant, Ulysses S.) laid siege on both land and water, and by early July 1863 the Confederate defenders were suffering from starvation and exhaustion. On July 4 Pemberton accepted Grant's terms for surrender. Shortly thereafter he resigned his commission as lieutenant general and served out the balance of the war as an ordnance inspector with the rank of colonel.

After Appomattox, Pemberton retired to a farm near Warrenton, Va. In 1876 he moved to Philadelphia.