High school student Maki Sasahara is an otaku who prefers the predictability of his two-dimensional romances to the messiness of real-life relationships. Despite his desire to avoid the spotlight, he finds himself drawn into the orbit of his popular and outwardly carefree classmate, Shinjo. Shinjo has a problem he believes Maki is uniquely qualified to solve: he has developed feelings for a male biology teacher and needs advice on how to confess. Reluctantly, Maki agrees to help, using his extensive knowledge from manga and games to coach Shinjo through his romantic pursuit.

As the two spend more time together, the dynamic of their relationship shifts. The story follows Maki’s internal struggle as he moves from annoyance to a dawning awareness of his own feelings for Shinjo, a situation complicated by his complete lack of real-world romantic experience. This awakening forces Maki to confront the gap between the fictional love stories he cherishes and the confusing, high-stakes reality of his own burgeoning emotions.

The central conflict arises from the characters’ mutual inexperience and misunderstandings. While Shinjo initially appears to be a confident "real-life person" (riajuu), he is just as clumsy and uncertain about love as Maki. The narrative arc traces Maki’s journey from self-doubt and denial to a clumsy, headlong attempt to win Shinjo’s affection, leading to a series of awkward and comedic confrontations. The story culminates in a period of emotional turmoil after a failed confession, exploring the raw and often embarrassing reality of first love.

Shinjo-kun to Sasahara-kun is set in a contemporary Japanese high school and serves as a spin-off focusing on the younger brother of the couple from the manga Samejima-kun to Sasahara-kun. The main characters are Maki Sasahara, an introverted otaku whose defenses are broken down by his first real crush, and Shinjo, a popular student whose genuine and persistent nature eventually wins Maki over. The story includes notable appearances from the characters of the parent series, providing fans with a continuation of their story from a new perspective.