Nagisa is a petite framed boy with light blue hair and azure eyes. His hair goes past his shoulders due to his mother forcing him to keep it that way. He kept it in a pony tail until Kaede Kayano joined the classroom and put it in two pigtails. He is known for his androgynous appearance which has often been poked fun at by many people - most notably, Rio Nakamura andKarma Akabane.
Seven years after graduation, his hair is noticeably shorter and no longer tied in a pigtail, though he still keeps his bangs.