Crocodylus anthropophagus was first named by Christopher A. Brochu, Jackson Njau, Robert J. Blumenschine and Llewellyn D. Densmore in 2010. The specific name anthropophagus is from Greek word "anthropos" that means "human" and Greek word "phagos" that means "eater", in reference to the evidence that this animal included hominids in its diet.