It has been a century since "true magic"—initially thought to be merely folklore and legend—had become commonplace technology worldwide. First National Magic University Affiliated High School (First High), one of the nine magic academies in Japan, admits two skilled siblings—Miyuki and Tatsuya Shiba—into the academy. First High splits its students into two groups, Course 1 and Course 2, based on entrance exam scores. This causes an apparent disdain for the Course 2 students, as they are labeled "Weeds" by Course 1 students, who alternatively call themselves "Blooms."

Tatsuya is admitted to Course 2, while his sister Miyuki joins Course 1 as an honor student. Miyuki wishes to show First High that, despite her brother being labeled as inept, he is among the best magicians in the whole world.

Mahouka Koukou no Yuutousei retells the story of Mahouka Koukou no Rettousei from the point of view of Miyuki and the other female characters.