The question seems a bit broad, but if we’re talking about a popular light novel series with an academy setting and a genius swordsman, I immediately think of 'The Irregular at Magic High School'. The main characters are the siblings Tatsuya and Miyuki Shiba. Tatsuya is the genius—technically not a swordsman in the traditional sense, but his combat skills with his specialized CAD and his 'Regrowth' ability are insane. He’s the underrated irregular. Miyuki is the acclaimed prodigy with incredible magical power. Their dynamic, with her intense devotion to him and his quiet, protective nature, really drives the story.
That said, the 'genius swordsman' archetype is everywhere. In 'Chivalry of a Failed Knight', you’ve got Ikki Kurogane, the 'Worst One' who becomes an unstoppable swordsman through sheer skill, not raw magic power. His rivalry and relationship with Stella, the 'Crimson Princess', is the core. For a more classic fantasy take, 'The Rising of the Shield Hero' has Raphtalia, who grows from a scared child into a master swordswoman under Naofumi’s wing, though the academy element is less prominent there. It really depends on which specific story you’re curious about.