Influenza A (H1N1) infection has been noted to be common in the young and high-risk groups for influenza infection, including transplant candidates and recipients. However, the optimal dosage and duration of oseltamivir for severely immunocompromised patients have not been defined. We report the case of a patient with relapsed neuroblastoma who was infected with influenza A (H1N1) and suffered from skin and lung graft versus host disease after he had received allogeneic hematopoietic stem cell transplantation from a matched sibling donor. During the immunosuppressant therapy, he was diagnosed with influenza A (H1N1) infection by real time polymerase chain reaction (RT-PCR). He recovered after oseltamivir treatment with a dosage of 90 mg twice a day for two weeks, which was two times of the standard dose until influenza A (H1N1) RT-PCR was proven to be negative.