We report a case of 65 years old man who was found on routine esophagogastroduodenoscopy to have gastric tumour. Histology revealed adenocarcinoma. Staging investigation with abdominal computed tomography (CT) confirmed gastric cancer of the antrum with lymph node enlargement at hepatoduodenal ligament. The patient underwent laparoscopic assisted distal gastrectomy with D2 lymphadenectomy. Pathology revealed intestinal type moderately differentiated tubular adenocarcinoma invading lamina propria (pT1a). Four positive lymph nodes out of 34 did not show metastatic adenocarcinoma but rather Squamous Cell Carcinoma (SCC) and were positive for p63 and CK5/6 on immunohistochemistary. Primary site of SCC was not found. He received adjuvant chemotherapy with TS-1 60 mg. After two years of follow-up he is asymptomatic and repeated EGD and abdominal CT Scan were normal. Herein, the authors report the case of early gastric cancer with synchronous metastatic SCC with unknown primary site.