"So Cute It Hurts!!" is a romantic comedy manga series that revolves around the lives of twin siblings Megumu and Mitsuru Kobayashi, who have strikingly different personalities despite their identical appearances. Megumu is a cheerful, outgoing girl with a passion for history, while Mitsuru is a brooding, delinquent-type boy who excels in academics but avoids social interactions. Their lives take an unexpected turn when Megumu convinces Mitsuru to switch places with her so she can attend an all-boys school to pursue her crush, Aoi Sanada, a history enthusiast. Simultaneously, Mitsuru reluctantly agrees to attend Megumu's all-girls school to avoid his own problems.

At the boys' school, Megumu, disguised as Mitsuru, encounters Aoi, who is initially cold and aloof but gradually warms up to her. Meanwhile, Mitsuru, posing as Megumu, struggles to navigate the complexities of the girls' school, where he meets Shino Nishihara, a kind and perceptive girl who becomes suspicious of his true identity. As the twins navigate their swapped lives, they face challenges such as maintaining their disguises, dealing with rivalries, and uncovering secrets about their classmates. The story explores themes of identity, self-discovery, and the bonds between siblings, as both Megumu and Mitsuru grow through their experiences.

The narrative is driven by a mix of humor, misunderstandings, and heartfelt moments, with a focus on the evolving relationships between the characters. Aoi's mysterious past and his connection to historical events add depth to the plot, while Shino's interactions with Mitsuru provide emotional resonance. The series balances lighthearted comedic elements with more serious undertones, creating a dynamic and engaging storyline. Through their adventures, the twins learn valuable lessons about love, friendship, and the importance of being true to oneself.