Rakudai Kishi focuses on Ikki Kurogane, a descendant from a prestigious clan of Blazers, who now studies in one of seven Blazer-affiliated schools in Japan, Hagun Academy, as a repeater.

[Blazers are gifted people who has the ability to materialize weapons and utilize magic. Under a worldwide set of regulations for Blazers, Blazers are required to study to be "professional" Blazers called Mage-Knights, who are allowed to return to society to assume regular occupations or to fight rogue Blazers in anti-crime and anti-terrorism units.]

Despite his background, Ikki is unable to graduate because the strong influence of the Kurogane family manipulates the system used in the school so that he doesn't acquire his license as a legitimate Mage-Knight, something that stemmed from Ikki's "poor" Blazer abilities (and you can say the family's immense ego). Of course, the rest of the school don't know this, so he is instead called the "Worst One" for being the last in the scholastic rankings.

He meets one of the strongest Mage-Knights in Hagun Academy, Stella Vermillion, in an embarrassing encounter, and the foreigner princess challenges him to a clean duel, but eventually gets defeated when Ikki shows his ability to replicate the swordsmanship of an enemy to counter her attacks. Because she lost, the current headmaster and a radical leader who opposes the injustices committed to Ikki, Kurono Shinguuji, permits the two to share the same room. Kurono also reveals that she has made a deal with Ikki, allowing him to graduate IF he wins the Seven Stars Sword Festival, a Mage-Knight tournament that pits the strongest among the seven Mage-Knight academies in Japan.

Stella eventually learns of Ikki's struggles as a boy betrayed by his own family, and she also exposes her past as a girl who simply wants someone to properly acknowledge her true strength. Their relationship blossoms since that moment of understanding.