The Charleston area first experienced Civil War hostilities during the September 1861 campaign that culminated in a Union victory at the Battle of Carnifex Ferry on the Gauley River in Nicholas County. Federal forces controlled the region until the following summer, when the Confederacy made plans to recover the Kanawha Valley after General Thomas "Stonewall" Jackson's successful Shenandoah Valley campaign. On August 11, 1862, Union General Jacob D. Cox and about 5,000 Kanawha Division troops were reassigned to the defense of Washington, leaving an undersized force of around 5,000 Union soldiers in the Kanawha Valley under Colonel Joseph A. J. Lightburn.

Confederate Major General William W. Loring moved quickly to retake the area which was a source of the precious salt needed for meat preservation. On August 22, he dispatched Brigadier General Albert G. Jenkins on a daring cavalry raid north of the Kanawha Valley. The Jenkins raid proved that Union defenses were indeed inadequate. Then, on September 6, Loring led 10,000 Confederates north from Pearisburg, Virginia, to confront the weakened Federals. His army drove back Union troops near Fayetteville on September 10, and the next day engaged a withdrawing force along the James River & Kanawha Turnpike at Camp Piatt, present-day Belle. On September 12, Loring's advance units reached the south side of Kanawha River just east of Charleston, near the present University of Charleston campus.

Early Saturday morning, September 13, 1862, Charleston residents awoke to the sound of Confederate artillery shelling Union forces east of town. The Rebel guns were later moved to Fort Hill where they began a heavier bombardment. Federal troops countered with a weak barrage from a six-pound gun stationed near a barn on the Ruffner estate along Kanawha River in Charleston's present East End. Union gunners also deployed a force to Cox's Hill (near present Spring Hill Cemetery) to the north and commenced firing from there. Meanwhile, a spirited ground engagement took place near the site of the present State Capitol, one mile east of the present downtown but then outside the city.

About 11:30 a.m., Union troops withdrew to the area of present downtown Charleston. Colonel Lightburn notified civilians to evacuate the town and warned the Ruffner family to leave their homes along present Kanawha Boulevard. Confederates reached downtown around 3:00 p.m. and captured the Union garrison flag. In advance of his outnumbered army's withdrawal, Lightburn ordered his Union troops to torch a number of downtown buildings rather than having them fall into enemy hands. They included Asbury Chapel, which had served as a quartermaster's store, the Kanawha House Hotel, Bank of Virginia, Mercer Academy, two stores, and several warehouses and cavalry barns. Retreating Federals then crossed the suspension bridge that carried present Washington Street across Elk River and cut the bridge cables to slow pursuing Confederates. Dueling artillery batteries kept up a fierce bombardment west of the Elk until 5:00 p.m. and infantry skirmishes continued until dark, when the fighting ended.

Despite suffering a military defeat against superior odds, Union Colonel Joseph A. J. Lightburn is credited with maintaining a continual skirmish line along the 50-mile retreat to Point Pleasant, while keeping his 700-wagon supply train worth an estimated one million dollars from falling into enemy hands. Unionist townsfolk and liberated local slaves joined in "Lightburn's Retreat," filling the Kanawha River with boats of all kinds and clogging the roads. The Confederate occupation lasted scarcely six weeks before Federals reoccupied the valley for the duration of the war.

Confederate casualties in the 10-day Kanawha Valley Campaign numbered 18 killed and 89 wounded, while Union forces reported 25 killed, 95 wounded, and 190 missing.