Professor Utonium (voiced by Tom Kane) is a scientist who created the super heros known as The Powerpuff Girls. The Professor once housed a chimpanzee named Jojo (later to become the girls' arch-enemy, Mojo Jojo ) as a lab assistant who proved to be reckless and destructive. Jojo pushed the Professor while he was stirring his Perfect Girl concoction, causing him to accidentally break through a glass containing the mysterious "Chemical X", which spilled into the formula, thus creating the Powerpuff Girls. The Professor is a genius in many fields of science, having shown knowledge in fields such as physics, chemistry, and biology as well as being a skilled inventor.

It is believed by fans that the Professor's design was re-altered and used for the character Jack from Samurai Jack as both characters looked surprisingly similar.