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.

Throughout the fall, his men harassed Union troops and supply lines, including the vital Baltimore and Ohio Railroad.

Jenkins led his men through the Cumberland Valley into Pennsylvania and seized Chambersburg, burning down nearby railroad structures and bridges.

During their invasion of Pennsylvania, his brigade, under Jenkins' direction, abducted hundreds of African Americans (most of them free people of color with a few being fugitive slaves), all of whom were forcibly sent southwards and sold into slavery.

[3] He accompanied Ewell's column to Carlisle, briefly skirmishing with Union militia at the Battle of Sporting Hill near Harrisburg.

Jenkins did not recover sufficiently to rejoin his command until fall, and spent the early part of 1864 raising and organizing a large cavalry force for service in western Virginia.

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.