Childhood best friends Nao Mamiya and Kyousuke Miyoshi have always competed against each other, whether in academics and sports or trivial day-to-day things. Despite Nao winning every time, Kyousuke refuses to give up, hoping to defeat him in the future.

One day, however, at the age of 17, Nao is struck by a sudden illness and is hospitalized for several weeks, only to return as an "emerged" female. Much to the dismay of Kyousuke who is afraid of women, Nao easily accepts the situation and is ready to continue living life as a girl.

In a world where a gender shifting mechanism maintains a fixed male-to-female ratio, Kanojo ni Naru Hi is the tale of Nao as a boy who has switched genders, adapting to the change in his circumstances.