Background Carcinoid tumors are usually considered to have a low degree of malignancy and show slow progression. One of the factors indicating the malignancy of these tumors is their size, and small ampullary carcinoid tumors have been sometimes treated by endoscopic resection. Case presentation We report a case of a 63-year-old woman with a minute ampullary carcinoid tumor that was 7 mm in diameter, but was associated with 2 peripancreatic lymph node metastases. Mild elevation of liver enzymes was found at her regular medical check-up. Computed tomography (CT) revealed a markedly dilated common bile duct (CBD) and two enlarged peripancreatic lymph nodes. Endoscopy showed that the ampulla was slightly enlarged by a submucosal tumor. The biopsy specimen revealed tumor cells that showed monotonous proliferation suggestive of a carcinoid tumor. She underwent a pylorus-preserving whipple resection with lymph node dissection. The resected lesion was a small submucosal tumor (7 mm in diameter) at the ampulla, with metastasis to 2 peripancreatic lymph nodes, and it was diagnosed as a malignant carcinoid tumor. Conclusion Recently there have been some reports of endoscopic ampullectomy for small carcinoid tumors. However, this case suggests that attention should be paid to the possibility of lymph node metastases as well as that of regional infiltration of the tumor even for minute ampullary carcinoid tumors to provide the best chance for cure.