We don't know, it's never been officially stated. In the original text, Chrona's never explicitly referred to as he or she.
Honestly though, all signs point towards Chrona more likely being a girl. Ragnarok lifting up her dress, squeezing her chest, one of her outfits had an emphasize on the chest area, and really, she just looks more like a girl than a guy.
It could still be an extremely feminine guy, but who knows.