While gender truly has no importance in this game, there seems to be a lot of debate about whether or not Bonnie is a boy or a girl. Many fans had been confused due to Bonnie's name in the original, and Toy Bonnie just added more confusion due to his eyelashes and seemingly "face full of makeup."

However, the creator of the game, Scott Cawthon, has stated a number of times that, when he designed Bonnie (and Toy Bonnie), he designed them to be male.