In 1861, near the beginning of the American Civil War, Atkinson established the "Hampden–Sydney Boys" and served as their captain, Company G, 20th Virginia Regiment. The troop was assigned to Col. John Pegram's Brigade, Gen. Robert Garnett's command and fought in early battles including both Big Bethel and Rich Mountain. At the battle of Rich Mountain, July 11, 1861, the Hampden–Sydney Boys were captured. After a nearly two-hour fight, the Union forces split the Confederate forces and the latter retreated from Lauren Hill, resulting in the capture of Col. John Pegram's command. The Hampden–Sydney Boys were paroled with the direction not take up arms again and that they return to their studies.