Because the Jedi Coalition had originally used it as a hidden base on Shedu Maad during the war after they had evacuated their temporary base on Endor, its location was still a closely guarded secret.
While the Jedi Order was reestablishing itself after the volatile war, they left the academy open while the Ossus facility was being repaired, due to the fact that all other academies had remained closed, to ensure the safety of the younglings. After several Jedi contracted Force psychosis, Leia Organa Solo smuggled four Jedi, Natua Wan, Seff Hellin, Yaqeel Saav'etu, and Bazel Warv to the academy, to prevent them from being frozen in carbonite, like Jysella and Valin Horn.