The non-Langerhans cell histiocytosis (LCH) juvenile xanthogranulomatosis (JXG) is usually a benign disease limited to the skin. Only a few cases of systemic disease with at least two affected organs and lethal outcomes have been reported to date. Treatment is controversial and no standard protocol is available. We report the rare case of a 22-month-old boy presenting multiple erythematous brownish papules of the head, trunk and legs, which had developed starting from his 6th month of life. Additional symptoms were delayed psychomotor development, hydrocephalus and hepatosplenomegaly. Further diagnostics revealed a systemic JXG with involvement of the skin, central nervous system, liver and spleen. The patient did not respond to initial therapy with prednisone and vinblastine according to protocol III for LCH. However, further therapy with cytarabine and 2-chlorodeoxyadenosine followed by a consolidation phase with 2-chlorodeoxyadenosine alone was successful and the patient is in his 4th year of remission. We provide a comprehensive review of the reported cases of systemic JXG to date.