The fossa navicularis is a notch-like bone defect in the basiocciput that has been hitherto considered as an anatomical variant of the clivus and not previously described as a potential source of clival or skull base pathology. We report the imaging findings in a 5-year-old child who presented acutely with a retropharyngeal abscess and osteomyelitis of the clivus. Imaging after treatment revealed a "notch-like" defect in the anterior clivus consistent with a fossa navicularis. Based on these appearances, we postulate that the lymphoid tissue of the pharyngeal tonsil residing in the fossa navicularis served as a route through which infection spread and subsequently developed into clival osteomyelitis, which is a rare diagnosis. This case is unique, and we believe that the presence of this variant in young children may be important and is not merely an anatomical curiosity.