Generalized lymphatic anomaly is a multifocal lymphatic malformation that affects the skin, thoracic viscera, and bones. A 3year-old Japanese boy presented with right facial palsy due to cystic tumors in the ipsilateral petrous bone. Pericardial effusion had been found incidentally and generalized lymphatic anomaly had been diagnosed by pericardial biopsy. Petrous bone tumor had been followed up without surgery. At the age of seven he presented with fever and disturbance of consciousness, and bacterial meningitis due to Streptococcus pneumoniae was diagnosed. Computed tomography and magnetic resonance imaging revealed middle skull-base leakage due to lymphatic malformation. He achieved complete recovery under intensive care with antibiotics and mechanical ventilation. One year later, he presented with multiple cystic formations in bilateral femora. At the 3-year follow-up, the patient was healthy with no recurrence of meningitis and osteolytic lesions in the femora were non-progressive. Computed tomography and magnetic resonance imaging are useful for demonstration of skull-base leakage by generalized lymphatic anomaly. We should consider generalized lymphatic anomaly among the differential diagnoses for skull-base leakage.