With the outbreak of the Civil War Lee became a captain in the Confederate Army cavalry and was soon promoted to major. He initially served in western Virginia under the command of Brig. Gen.William Loring during 1861 and early 1862. He was then placed under the command of Maj. Gen.J.E.B. Stuart, becoming a lieutenant colonel, and later colonel in the 9th Virginia Cavalry.
After the Battle of South Mountain, Lee was promoted to brigadier general. He fought at Antietam under the command of Brig. Gen. Fitzhugh Lee, his cousin. He commanded the 3rd Brigade of Stuart's Cavalry Division at the Battles of Fredericksburg and Chancellorsville. He was wounded during combat at Brandy Station at the beginning of the Gettysburg Campaign and was captured by Union forces at Hickory Hill, Virginia, two weeks later, while recuperating. He was a prisoner of war in New York State until returned to the Confederate Army on February 25, 1864. To accomplish this he was exchanged for Confederate captive Union Brig. Gen. Neal S. Dow. In April, he was promoted to major general and commanded a division in the Cavalry Corps during the breakout from Petersburg and the retreat of his father's army in the Appomattox Campaign. By the end of the war, he had risen to second-in-command of the Confederate cavalry. He surrendered along with his father at Appomattox Court House.
Post-War career
Lee returned to White House Plantation and planting after the war. Nearby, his younger brother Rob lived at Romancock Plantation across the river in King William County.
Lee married twice, first in 1859 to Charlotte Wickham, a descendant of attorney John Wickham. They had two children, a boy and a girl, both of whom died in infancy. Charlotte died in 1863.
On November 28, 1867, he married Mary Tabb Bolling, a descendant of ColonelRobert Bolling and his second wife Anne Stith. They had two children who lived to adulthood: Robert Edward Lee, born 11 Feb 1869 at Petersburg, and George Bolling Lee, born 30 Aug 1872 at Lexington.
Lee is the step-great-great-grandson of George Washington. Lee's mother, Mary Anna Randolph Custis Lee, was the great-granddaughter of Martha (Dandridge) Custis, who was a widow living at her White House Plantation in New Kent County (which Rooney Lee later inherited) when she was courted by Colonel George Washington before their marriage in 1759.