A 1-year-old girl with familial hemophagocytic lymphohistiocytosis underwent umbilical cord blood transplantation. On day 24, she developed renal failure, jaundice and hemolytic anemia, and we diagnosed transplantation-associated thrombotic microangiopathy (TMA). Despite discontinuation of tacrolimus, her condition became even worse. From day 25, we started to administer recombinant human soluble thrombomodulin (rTM). According to the recommendation of the pharmaceutical company, a dose reduction from 380 to 130 IU/kg/day in patients with renal failure, we administered rTM at the reduced dose during the first 2 days. Because the reduced dose was not effective, we administered rTM at the standard dose from day 27. Surprisingly, she began to recover from TMA on the next day, and we continued to administer rTM until day 109. She is alive without evidence of disease eighteen months after transplantation. Adverse events of rTM were severe gastrointestinal hemorrhage and hemorrhagic cystitis, and it was necessary to control hemorrhage by interruption of administration. This case report suggests that rTM may be effective for TMA. Moreover, alteration in the dosage schedule seems to be required according to the condition of patients. Further studies are needed to evaluate the effectiveness and an optimal dose of rTM as a treatment for TMA.