On May 16, 1861, Cooper was promoted to full general in the Confederate Army. He was one of five men promoted to the grade at that time and one of only seven during the war, but with the earliest date of rank. Thus, despite his relative obscurity today, he outranked the better-known confederates Albert Sidney Johnston, Robert E. Lee, Joseph E. Johnston, and P. G. T. Beauregard.Eicher, p. 807. Generals (ACSA) Line Command List Cooper reported directly to Confederate President Jefferson Davis. At the war's end in 1865, Cooper surrendered and was paroled on May 3 at Charlotte, North Carolina.
