"Hiyokoi" centers on Hiyori Nishiyama, a shy and petite high school girl who returns to school after a long absence due to a traumatic accident. Struggling with social anxiety and self-doubt, Hiyori finds it difficult to interact with her classmates. Her life begins to change when she meets Yuushin Hirose, a tall, outgoing, and kind-hearted boy who sits next to her in class. Despite their contrasting personalities, Yuushin takes an interest in Hiyori and gradually helps her come out of her shell.

The narrative explores Hiyori's journey of self-discovery and her efforts to overcome her fears. Through her interactions with Yuushin and other classmates, she begins to build confidence and form meaningful relationships. The story also delves into Yuushin's perspective, revealing his own vulnerabilities and the reasons behind his supportive nature. Their growing bond is marked by moments of warmth, humor, and occasional misunderstandings, reflecting the complexities of teenage emotions.

Secondary characters, such as Hiyori's childhood friend Ritsuka and Yuushin's friend Sou, add depth to the story by providing additional perspectives and contributing to the dynamics of the group. The series balances lighthearted school life moments with more introspective scenes, capturing the challenges of adolescence and the importance of empathy and connection. Themes of friendship, personal growth, and the courage to face one's fears are woven throughout the narrative, making "Hiyokoi" a heartfelt exploration of young love and self-acceptance.