With the outbreak of the Civil War and Virginia's subsequent secession, Jenkins resigned from Congress in early 1861. He raised a company of mounted partisan rangers, which by June was enrolled in the Confederate Army as a part of the 8th Virginia Cavalry, with Jenkins as its colonel. By the year's end, his men had become such a nuisance to the Federals in western Virginia that military governor Francis H. Pierpont appealed to President Abraham Lincoln to send in a strong leader to stamp out the rebellion in the area. Early in 1862, Jenkins was elected as a delegate to the First Confederate Congress. After promotion to brigadier general on August 1, 1862, he returned to active duty. Throughout the fall, his men harassed Union troops and supply lines, including the vital Baltimore & Ohio Railroad. In September, Jenkins's cavalry raided northern Kentucky and now West Virginia. They briefly entered extreme southern Ohio near Buffington Island, becoming one of the first organized Confederate units to enter a Northern state. In December, Robert E. Lee requested that Jenkins and his men transfer to the Shenandoah Valley. After spending the winter foraging for supplies, he led his men on a raid in March 1863 through western Virginia, seeking to influence the popular vote which ultimately created the state of West Virginia. During the Gettysburg Campaign, Jenkins' brigade formed the cavalry screen for Richard S. Ewell's Second Corps. Jenkins led his men through the Cumberland Valley into Pennsylvania and seized Chambersburg, burning down nearby railroad structures and bridges. He accompanied Ewell's column to Carlisle, briefly skirmishing with Union militia at the Battle of Sporting Hill near Harrisburg. During the subsequent Battle of Gettysburg, Jenkins was wounded on July 2 and missed the rest of the fighting. He did not recover sufficiently to rejoin his command until fall. He spent the early part of 1864 raising and organizing a large cavalry force for service in western Virginia. By May, Jenkins had been appointed Commander of the Department of Western Virginia with his headquarters at Dublin. Hearing that Union Brig. Gen. George Crook had been dispatched from the Kanawha Valley with a large force, Jenkins took the field to contest the Federal arrival. On May 9, 1864, he was severely wounded and captured during the Battle of Cloyd's Mountain, a Union victory which destroyed the last railroad line connecting Tennessee and Virginia.
Death and legacy
A Union surgeon amputated Jenkins' arm, but he never recovered, dying twelve days later. He was initially buried in New Dublin Presbyterian Cemetery. After the war, his remains were reinterred at his home in Greenbottom, near Huntington, West Virginia. He was later reinterred in the Confederate plot in Spring Hill Cemetery in Huntington. Jenkins's home, Green Bottom, has been restored and is now a museum run by the West Virginia Division of Culture and History. In 1937, Marshall University constructed Jenkins Hall, naming it in honor of the Confederate cavalry officer. In 2018, the university reviewed the name given Jenkins’ history as a slaveholder and a defender of slavery. They chose to keep the name while contextualizing the history of racism and slavery. On July 7, 2020, the Marshall University Board of Governors voted unanimously to remove the name from its education building. In 2005, a monument to General Jenkins was erected in Mechanicsburg, Pennsylvania, commemorating his service during the Gettysburg Campaign.
