Kanojo ni Naru Hi

Kanojo ni Naru Hi is a romance, gender-bender shoujo manga. It tells the story of two childhood friends who are always competing, Miyoshi and Mamiya. One day, Mamiya is hospitalized, and it is discovered that he was genetically born as a girl. And now, begins a life with Miyoshi and the female Mamiya.

Summary
From Baka-Updates Manga:

Miyoshi is always competing and losing against his childhood friend, Mamiya, who is good at everything. One day, Mamiya collapses from illness and is hospitalized for several weeks. When he returns to school, it turns out he is genetically female, and has decided to try living his life as a girl now much to Miyoshi's horror.

Plot
The first chapter touches on the friendly rivalry between Mamiya and Miyoshi. However, after Mamiya collapsed and got hospitalized, Mamiya comes out revealing 'himself' as a girl. This is due to a scientific genetic phenomenon in which the ratio of woman and man are the same. Mamiya lives out her life as a girl, while Miyoshi struggles to cope with her with his gynophobia. As Mamiya continues to help and intimidate him with her girly features, he recovers bit by bit from her gynophobia. Slowly, he falls in love with Mamiya.

In Chapter 2, it is shown that he has become more protective of Mamiya.