We describe the case of a 2-year-old girl with a primary left upper mediastinal neuroblastoma with bone metastasis. She underwent autologous peripheral blood stem cell transplantation following chemotherapy with high-dose busulfanmelphalan. On day 61, she developed pulmonary hypertension with generalized fatigue and hypoxemia. On day 91, she was diagnosed with transplant-associated thrombotic microangiopathy(TA-TMA)secondary to anemia, red cell fragmentation, thrombocytopenia, and elevated serum creatinine levels, and her pulmonary hypertension worsened. She underwent cardiac catheterization and was diagnosed with pulmonary arterial hypertension(PAH). Management of fluid balance led to improvement in TA-TMA, and oxygen therapy was initiated for PAH. On day 131, she developed cardiac arrest secondary to pulmonary hypertensive crisis. Although she was successfully treated with multidisciplinary therapy, she had neurological sequelae. PAH improved following treatment with sildenafil and bosentan. PAH and TA-TMA are serious complications that may occur owing to vascular endothelial damage after hematopoietic stem cell transplantation. Clinicians must be vigilant for TA-TMA in patients who develop PAH after hematopoietic stem cell transplantation.