He's a boy, they were trying to pull characters and personalities from all stages of life. (Ex. Toboe is the child, Hige is like the teenager, Tsume, is the father figure, and Kiba is the 더 많이 mature adult.) Toboe's sole purpose is to make 당신 understand that when 당신 are wiping out a species, everyone is affected and has to survive, even the children.
Toboe looks like a girl because children often do look androgynous, when one is little if 당신 are dressed as a boy and have not "developed" in anyway but 당신 were a girl 당신 would be mistaken easily for a boy, and vice versa.
Also, 아니메 artists 사랑 throwing Bishonens (beautiful young boys with pretty feminine features.) in to stories.
