We report here a 16-year-old male with primitive neuroectodermal tumor (PNET)-associated probable microangiopathy with multiple bone metastases. Laboratory findings excluded the possibility of amegakaryocytic or immune thrombocytopenia and/or disseminated intravascular coagulation. He was first treated with plasma-exchange (PE), followed by platelet transfusions, steroid pulse therapy and combined chemotherapy. PE and steroid pulse therapy reduced his plasma CRP level. Combined chemotherapy drastically increased his platelet count until it had almost normalized without further transfusion. The plasma level of von Willebrand factor-cleaving protease (ADAMTS13) activity measured before PE was not severely deficient (48% of normal) and an unusually large von Willebrand factor multimer (UL-VWFM) was detected. We consider that this therapeutic strategy has the following benefits: (1) reduction of plasma levels of factors that are harmful to both platelet activation and endothelial cell injury; and (2) the safe transfusion of platelet concentrate in thrombotic microangiopathy. This strategy should be confirmed in further cases.