The Confederate army did not have a single permanent overall field commander for most of the Civil War; instead, leadership shifted between the Confederate president and senior generals.

Direct answer

  • Jefferson Davis served as commander‑in‑chief of all Confederate land and naval forces in his role as president of the Confederate States, setting overall strategy for the Confederate armies throughout the war.
  • Robert E. Lee briefly acted as Davis’s principal military adviser and was “charged with the conduct of military operations in the armies of the Confederacy” in early 1862.
  • Only very late in the war, in February 1865, Robert E. Lee was formally appointed “General in Chief of the Armies of the Confederate States,” making him the top military commander of all Confederate armies from January–April 1865, while he still directly led the Army of Northern Virginia.

So, if you are thinking of the officer most closely associated with commanding the Confederate army as a whole, the answer is Robert E. Lee, especially in his role as General in Chief in 1865 , under the ultimate civilian command of President Jefferson Davis.