Kentei Gakuin no Magan Kenja

A cataclysm nearly wiped out life on Earth ten years before the story begins. Lag Logline, a magical prodigy, is named "sage" and put into a time-freezing spell to stop the world from ending one thousand years later. When he wakes, the world has changed completely. He encounters Clau, a swordswoman, and learns that magic is unknown in this future. Mistaken for a swordsman, Lag joins the Imperial Sword Academy to uncover the truth and keep his vow to save humanity.