Nogizaka Haruka no Himitsu centers around Yūto Ayase and Haruka Nogizaka. Yūto is seemingly ordinary, but Haruka is attractive, intelligent, and rich, which prompts other students to idolize her. One day, Yūto wanders into the school library in order to return a book and accidentally stumbles upon Haruka's deepest, darkest secret: she is a diehard fan of anime and manga, in other words, a regular otaku. Promising Haruka to keep this a secret, Yūto becomes her advisor and confidante of sorts.