On March 21, 1861, Pender resigned from the U.S. Army and was appointed a captain of artillery in the Confederate States Army. By May he was a colonel in command of the 3rd North Carolina Infantry (also designated the 13th North Carolina) and then the 6th North Carolina. Tried in combat successfully in the Battle of Seven Pines in June 1862, he was promoted to brigadier general and command of a brigade of North Carolinians in Maj. Gen. A.P. Hill's "Light Division". Confederate President Jefferson Davis personally promoted Pender on the Seven Pines battlefield.