A congenital cholesteatoma arising from the petrous pyramid is rarely encountered, and we report a case of such a cholesteatoma in a 23-year-old male. This cholesteatoma was successfully removed by a middle cranial fossa approach. The cholesteatoma showed a unique mode of spread, that is, it originated from the pyramidal apex and extended in two directions: through the facial canal to the tympanic sinus, and along the tympanic tegmen to the mastoid antrum. We discuss the importance of CT and MRI for achieving a diagnosis, as well as the merits of using a middle cranial fossa approach for the surgical excision of this cholesteatoma.