High school student Misaki Takahashi comes home to find his older brother being caressed by a stranger. Shocked by this scene, Misaki learns the man is Akihiko Usami, a famous novelist and his brother's closest friend. As the two grow closer, Akihiko becomes Misaki's private tutor. But after Misaki discovers the author's latest boys-love novel, he starts to doubt Akihiko's intentions regarding his friendship with the student's brother.
Meanwhile, Hiroki Kamijou, a university professor of classical literature and Akihiko's friend, mourns a failed relationship. On the verge of a mental collapse, he meets student Nowaki Kusama, who seeks his help for an upcoming exam. Despite repeatedly turning Nowaki down, Hiroki eventually agrees to assist. As they grow closer, more truths about the student come to light.
Furthermore, wealthy teenager Shinobu Takatsuki learns that his older sister has divorced Hiroki's coworker You Miyagi. He immediately wants to date the same man—who saved Shinobu from a robbery three years prior. However, You does not reciprocate and tries to drive him away. But the educator soon realizes that Shinobu will stop at nothing for their fated romance.
Junjou Romantica gathers three love stories, chronicling each couple's romance.