A 62-year-old man was diagnosed with esophagogastric junction cancer following esophagogastroduodenoscopy in response to hematemesis. Although liver metastasis was detected during surgery, a total gastrectomy and lower esophagus resection for local control was performed. Alpha-fetoprotein(AFP)-producing tumor with hepatoid adenocarcinoma was diagnosed on the basis of the pathological examination. Serum AFP levels remained high postoperatively and multiple liver metastases were detected on computed tomography imaging. After 6 courses of chemotherapy with S-1 and cisplatin (CDDP), a significant reduction in the size of the liver metastases and a decrease of serum AFP levels were achieved. Postoperative 2-year tumor control using S-1 single agent chemotherapy was obtained. AFP-producing esophagogastric junction cancer has a poor prognosis. This case raises the possibility that long-term survival can be obtained by combining surgery for local control with systemic chemotherapy.