The intraductal growth of nonfunctioning pancreatic endocrine tumors (NFPTs) is considered to be rare, and in our survey of the English-language literature, we found only three cases to have been described previously. We herein report the case of a 36-year-old man with a malignant NFPT that uniquely grew within the lumen of the main pancreatic duct (MPD) and completely obstructed the MPD, as shown by endoscopic retrograde pancreatography (ERP). Endoscopic ultrasonography clearly detected the tumor with intraductal growth. In addition, positron emission tomography (PET), using 18F-fluorodeoxyglucose (FDG) and computed tomography (CT) with the same scanner (FDG-PET/CT) showed enhanced uptake of FDG in the tumor. A pylorus-preserving pancreaticoduodenectomy and regional lymphadenectomy were performed under the preoperative diagnosis of an NFPT. Microscopically, positive immunoreactions for synaptophisin and vasoactive intestinal peptide indicated neuroendocrine differentiation of the tumor, while in addition, metastasis to a lymph node along the common hepatic artery was also observed. The patient has survived for 6 months after the surgery without any evidence of recurrence or metastasis. Both ERP and FDG-PET/CT were thus found to be useful for predicting the malignant potential of an NFPT in the preoperative diagnosis.