Unbeknownst to Wynn, Revan had been captured by the Jedi during the war and his memory altered. Headed by a Headmaster, one of the academy's leaders following the Great Sith War was Jorak Uln, an early headmaster of the who was later succeeded by Uthar Wynn who operated the academy during Lord Revan's reign over the Empire. Its students during this time were either Force-sensitives looking to take a side in the conflict, or fallen Jedi, disillusioned with either the Jedi Order, the war or the Republic in general. When Darth Revan and Darth Malak reopened the academy upon their return as Sith Lords to train warriors for their Empire, classes resumed in the sublevels as they trained to fight in the Jedi Civil War. Despite the Academy's existence, the Jedi Order did not lead an assault on the facility after the conclusion of the war.Д«y the time of the Mandalorian Wars the entrance to the academy was the only surface level structure remaining, with sublevels being employed for the training of apprentices.

Following the Sith holocaust of 5,000 BBY, the temple's upper structures were ruined, but this did not prevent the academy from being fully operational as of 3,993 BBY. Established at the back wall of the Valley of the Dark Lords, the exact date of the Academy's founding is lost to history, tracing its roots back to at least the time leading up to the Great Sith War.

Knights of the old republic korriban