A Pennsylvania native of Quaker stock, John Clifford Pemberton was born on August 10, 1814. Despite his religious background John grew quite social and enjoyed parties, dances, and even the theater. Yet he was a quiet young man who shied away from intimacy and counted few close friends. (Among his boyhood friends was George Meade who was destined to command the Union forces at Gettysburg.) Pemberton's father, a close friend of President Andrew Jackson, secured an appointment to the United States Military Academy at West Point for his son and John embarked on a military career.

At West Point, Pemberton was an average cadet who did not excel academically and accrued demerits by the score. During his first class, or senior year, he was even arrested for violation of the academy's prohibition against the possession of alcohol. Only after the entire senior class signed a pledge to abstain from alcohol for the duration of their term were the charges dropped. At graduation in 1837, Pemberton stood 27th in a class of 50 cadets and was assigned to duty with the 4th U. S. Artillery.

Pemberton went on to serve in the Second Seminole War and Mexican War where he saw action at Palo Alto, Resaca de la Palma, and Matamoras. While serving in Mexico he met a young lieutenant who would play a prominent role in his life during the Civil War. His name was Ulysses S. Grant. During this same period he struck up a close friendship with yet another young officer, this one an ardent Mississippian named Jefferson Davis. Upon his return from Mexico, he married Martha Thompson, a native of Norfolk, Virginia, and a fervent supporter of Southern politics and customs, and the couple had seven children. Patty, as he affectionately called his wife, held tremendous sway over her husband. At the outbreak of the Civil War she wrote John, "My darling husband, why are you not with us? Jefferson Davis has a position for you." Not willing to tum against his wife's interests, on 24 April 1861 resigned his commission in the U.S. Army and sought service in the newly-forming Confederate army. Two of his brothers volunteered in the Union army.

Pemberton offered his sword to his wife's native state, Virginia and Gov. John Letcher appointed him a lieutenant colonel in the state's forces. After Virginia's admission to the Confederacy, Pemberton was elevated to brigadier general and sent to the Department of South Carolina and Georgia. He initially served there under Robert E. Lee, but when Lee was summoned to Richmond to serve as the president's military advisor, Pemberton was elevated to major general and placed in departmental command.

In this role, Pemberton sought to concentrate his available manpower which would necessitate opening coastal areas to enemy incursions. He even recommended the evacuation of Fort Sumter and quickly fell afoul of local officials and South Carolina Governor Francis Pickens who clamored for Pemberton's removal. In the fall of 1862, with little useful field or combat experience, Pemberton was named commander of the Department of Mississippi and East Louisiana and charged with defense of the Mississippi River and the twin bastions of Vicksburg and Port Hudson.

Throughout the winter of 1862-1863 he was successful in parrying enemy movements, but in the spring of 1863 events would soon prove that Pemberton had been elevated beyond his capacities to command as Union Maj. Gen. Ulysses S. Grant launched his successful campaign against Vicksburg. Despite a valiant defense throughout a 47 day-long siege of the city, Vicksburg surrendered on July 4, 1863. In the aftermath of siege, Pemberton voluntarily resigned his commission and accepted the lower grade of lieutenant colonel and remained in Confederate service for the duration of the war.