As rector of the Grace Church in Lexington, Virginia, Pendleton reluctantly joined the Confederate service in 1861. He became captain of the Rockbridge Artillery, but he was quickly promoted to colonel. By July, he was the Chief of Artillery for the newly organized Army of Northern Virginia. He demonstrated his skill at the Battle of First Manassas, then he was given a promotion to brigadier general. He was present during the Seven Days' campaign, but he failed to act quickly during the Battle of Malvern Hill, which won the displeasure of Lee. He subsequently failed to make accurate reports during the battles of South Mountain and Antietam. However, his success in his organization of the artillery was demonstrated with the success of the Battle of Fredericksburg. He served admirably throughout the rest of the war with the army from Chancellorsville to Appomattox as an administrator, and in command of the reserve artillery.