This report presents a case of primary pleomorphic rhabdomyosarcoma arising in the duodenum. A 63-year-old male with persistent melena was referred for a solid tumor in his right upper abdomen detected using ultrasonography. Gastrofiberscopy revealed a protrusion in the upper part of the duodenum, with a large ulcer on the top of it. Enhanced computed tomography showed that the tumor extended to the pancreas. Pancreaticoduodenectomy was performed, despite the absence of malignant cells in the biopsy specimen, with a preoperative diagnosis of duodenal cancer. The tumor consisted of multiple cell types, and immunohistochemical staining was positive for desmin, HHF-35 and alpha smooth muscle actin. Electron microscopy revealed primitive Z-band structures in the tumor. The final diagnosis was pleomorphic rhabdomyosarcoma of the duodenum. This is the first report of primary rhabdomyosarcoma occurring in the duodenum, confirmed by immunohistochemical staining and electron microscopy.