Juvenile xanthogranuloma (JXG) is a generally benign, self-limited histiocytic disorder, which belongs to non-Langerhans cell histiocytoses (non-LCH). However, systemic JXG can be fatal in rare cases. We present the case of an 11-year-old female with systemic JXG, who experienced repeated vertebral compression fractures and did not fully respond to systemic chemotherapy. Based on its reported efficacy in LCH, the patient underwent human leukocyte antigen-haploidentical hematopoietic stem cell transplantation (HSCT) with posttransplant cyclophosphamide. The patient did not suffer major complications and has not experienced relapse for 13 months since HSCT. HSCT may be a potential treatment option for patients with refractory non-LCH. K E Y W O R D S allogeneic hematopoietic stem cell transplantation, haploidentical HSCT with posttransplant cyclophosphamide, juvenile xanthogranuloma, non-LCH