At the start of the American Civil War, Omohundro attempted to join his older brother, Orville, in the Confederate Army. He was twice refused for his age, but was allowed to serve as a courier at the headquarters of the Virginia Militia under Major General John B. Floyd. Because of his youth and knowledge of the countryside, he became known as the "Boy Scout of the Confederacy". In February 1864, at the age of 17, he successfully enlisted as a private in Company G of the 5th Virginia Cavalry, part of the Army of Northern Virginia, and was soon serving directly in General J.E.B. Stuart's command as a courier and scout. At the Battle of Yellow Tavern, he delivered a scouting report to Stuart only minutes before the general was killed in battle. During the Battle of Trevilian Station, Omohundro was wounded and admitted to the Confederate States General Hospital in Charlottesville on June 20, 1864. After recovering from his injuries, and a short leave home, he returned to his company and scouted under the command of General Lunsford L. Lomax. Following the Third Battle of Winchester, the 5th Virginia Cavalry was consolidated with the 15th Virginia Cavalry, where Omohundro scouted under General Fitzhugh Lee during the last months of the war.