On the outbreak of the American Civil War, Otey left his job on the Virginia and Kentucky Railroad, and supposedly fired a cannon at Sewell's Point after Virginia seceded and actually hit a Union vessel, as well as fought with the U.S. Monticello on May 19, 1861. He became a lieutenant in Company S, 51st Virginia Infantry in the Army of the Kanawha under Col. Gabriel C. Wharton (VMI class of 1847, who had become a civil engineer in Arizona), former VMI mathematics professor Lt.Col. James W. Massie and former Virginia Governor General John B. Floyd (uncle of his fiancee, later wife). Otey served as a staff officer, and the 51st Virginia was tasked with protecting the Kanawha Valley and its salt and other mines, but had little success. The regiment suffered defeats at Carnifax Ferry and Cotton Hill in 1861 and in February 1862 at Fort Donelson, Tennessee, although only 2 members surrendered and the majority including this Otey escaped to defend Nashville. His three elder brothers also became Confederate officers: Kirkwood Otey commanded the 11th Virginia Infantry including at the Battle of Gettysburg (during which he sustained a shoulder wound); George Gaston Otey (who had begun the war as adjutant of the 1st Virginia Infantry) organized the "Otey Company" of light artillery in March 1862 which was sent to Western Virginia and east Tennessee and became the 13th Virginia Light Artillery by the war's end (after G.G. Otey died in October of wounds received at the Battle of Lewisburg in what became West Virginia in May); Walter Hays Otey of VMI's class of 1859 served with the 16th Virginia and 56th Virginia before resigning for health reasons and organizing a company of local defense light artillery at the Danville Arsenal.