Juvenile xanthogranuloma (JXG) is a rare benign disorder of unknown pathogenesis, usually a self-limited condition. Extracutaneous systematic involvement is infrequent. We report one of the few documented cases of congenital systemic JXG, presenting with fever, jaundice, hepatosplenomegaly, ascites, pancytopenia, and delayed skin involvement. Liver biopsy established the diagnosis and JXG was not demonstrated in the bone marrow. Rapid deterioration of liver disease and pancytopenia, prompted us to administer immunosuppressive treatment (Langerhans cell histiocytosis-II Protocol). The patient's clinical condition improved and visceral and skin lesions showed gradual involution. The patient is still free of disease 4 years after the initial presentation.