No, Nagito is not female.
Nagito Komaeda is a male character from the popular Danganronpa video game series. His physical attributes are clearly those of a young man; he is described as tall and skinny, possessing notably wide shoulders, sickly pale skin, and distinctive light gray-green eyes with thick eyelashes.
Character Identity in Danganronpa
Throughout his prominent role in Danganronpa 2: Goodbye Despair and other related media, Nagito's gender identity is consistently portrayed as male. His character design, voice acting, and narrative interactions with other students and events within the storyline firmly establish him as a male figure in the Danganronpa universe.