In 1861, "Rooney" Lee entered the Confederate service. He soon received an appointment as colonel of the 9th Virginia Cavalry. He was promoted to brigadier general in September 1862. In June, he was severely wounded at the Battle of Brandy Station. Consequently, he was captured and imprisoned by Union attackers during his recovery period. He was held until March 1864. Upon his return to the Confederate army, he was promoted to major general. In June 1864, he served in command of Confederate forces in the Battle of Staunton River Bridge. Four days later, on June 29th, he played an important role in the Battle of Ream's Station. At Appomattox, he served as the second in command of cavalry in the Army of Northern Virginia.