Poague returned to Virginia, and entered the Confederate Army as a second lieutenant in the famous Rockbridge Virginia Artillery. Poague was promoted to be that unit's captain by April 1862. With the battery, Poague fought at the battles of First Manassas, Romney, Kernstown, McDowell, and later with the Army of Northern Virginia in the Seven Days Battles, the Battle of Cedar Mountain, Second Manassas, the Battle of Harper's Ferry, Antietam, and Fredericksburg. Poague was promoted to major on March 2, 1863. He served as an executive officer to David G. McIntosh at the Battle of Chancellorsville, then was given his own battalion upon the formation of the Third Corps.