Boku to Kanojyo no XXX is about a shy and clumsy high school junior, Akira Uehara, who has a crush on his classmate, Nanako Momoi. Nanako Momoi is a the belle of the school, but that's only if she keeps her mouth close. When her mouth is open, she is rough, aggressive, and loud to the point that she drives admirers away. Akira Uehara's bestfriend, Shinnosuke Senbongi, advises Akira to give up on Momoi and find a new girl to like. Akira, however, can't do that because, although knowing that they are ill-matched, he feels that she is the one for him.
"Since the day I met her, I felt that she was my destiny" Akira Uehara about Momoi
Then, one day, (Nanako) Momoi calls in sick. Fortunately, for her classmates, Akira (Uehara) volunteers to deliver her homework to her house. After hearing a scream that sounds like Momoi's, Akira enters Momoi's house and winds up in her grandfather's lab. There, he sees Momoi tied up to be a test rat for her grandfather's new invention, a shrink machine. As he tries to save Momoi from being a lab rat, he finds himself instead tied to the machine replacing Momoi as the lab rat. Then, as Momoi straps Akira into the machine, her grandfather accidently pushes the machine's switch. Akira and Momoi are then zapped by the machine and wake up in each other's bodies. Both of them are surprised and want to return to their own bodies. However, they can not because the machine is broken and Momoi's grandfather does not have the money (nor the willpower) to fix it.
Until the machine is fix, Akira and Momoi agree to live as the other, but living as each other becomes difficult when they realize that their personalities are polar opposites. Their classmates in school start to notice the change in personalities, but instead of questioning it, the classmates actually favor it. Thanks to Momoi, the once weak and clumsy, but handsome Akira is now manly and straight-forward. On the other side, thanks to Akira, the once wild and loud, but adorable Momoi is now girly and elegant. Akira and Momoi fit the other's body so well that even their best friends, Shinnosuke Senbongi and Makoto Shiina, are attracted to their new selves.
To Akira's dislike, Momoi also realizes that her personality fits better in a guy's body and grows to like living as Akira. She can play rough basketball, work out, and go out with older ladies. She even falls for her best friend, (Makoto) Shiina, and starts dating her. Akira, however, wants to switch back. As much he loves being in the body of the girl he likes, he realizes that he cannot win Momoi's heart while being in her body. He also misses his family and his quiet life, since as Momoi, he now lives with an lazy grandfather and receives unwanted love advances from his best friend, Senbongi. How will Akira in Momoi's body adapt to this complex situation? Will he finally be able to persuade Momoi and switch back to his own body? Or will he give up on Momoi and accept his new life as a girl? Read the manga and find out.