Myeloid sarcoma (MS) is a tumor consisting of myeloid blasts that occurs at an anatomical site other than the bone marrow. We report the case of a 38-year-old man with duodenal MS who underwent an allogeneic bone marrow transplant in a non-complete remission (CR) state. After the transplant, residual disease was suspected on a fluorodeoxyglucose positron emission tomography (FDG-PET)/CT scan, and additional radiotherapy resulted in CR, which has been maintained for 21 months. FDG-PET/CT scanning is useful for evaluating residual myeloid sarcoma during the peritransplant period.