On the outbreak of the American Civil War Ewell resigned and joined the Confederate Army and commanded the 2nd Brigade at Bull Run (June, 1861). He also served under Thomas Stonewall Jackson in the Shenandoah Valley and at Manassas (August, 1862) and lost a leg at Groveton.
Ewell took over the defence of Richmond but was forced to withdraw on 3rd April, 1865. He was captured three days later at Sayler's Creek. Held in Fort Warren he was released on 19th August, 1865.
Richard Stoddert Ewell died at his farm near Spring Hill, Tennessee, on 25th January, 1872.