Lymphangioma localized to the bones of the skull base is rare. The authors report herein the case of a 5-year-old boy who presented with lymphangioma of the bone, localized to the skull base and leading to cerebrospinal fluid (CSF) rhinorrhea with meningitis. Neuroimaging demonstrated lytic destruction with a cyst in the right middle skull base. The patient was successfully treated with resection of the tumor and prevention of CSF leakage. Histopathological examination revealed a lymphangioma. An enlarging lymphangioma can lead to bone destruction. A differential diagnosis of a lytic lesion for a cyst at the skull base is important for proper case management.