Twins Megumu and Mitsuru Kobayashi study at separate schools—she in the girls" academy, he in the boys" school. Feeling confined by classmates of the same sex, they agree to exchange identities for a day. The ruse passes unnoticed at first, yet romance complicates matters. Their classmates notice odd habits, but none suspect the swap.
Kobayashi ga Kawai sugite Tsurai!! opens with a sincere confession from Megumu that leads her brother‑disguised self to share a kiss with senior Aoi Sanada. Aoi, who had never been comfortable around girls, begins to wonder if he is attracted to men. Meanwhile, Mitsuru encounters the proud queen of his school, Azusa Tokugawa, who finds herself heart‑throbbing in his (her) arms. The two pairs grow close, yet the twins" swapped identities remain hidden.