Merkel cell carcinoma (MCC) is a skin cancer that can also rarely arise in extracutaneous sites including mucosal surfaces. About 80% of MCCs harbor the Merkel cell polyomavirus (MCPyV). All cases of gastric MCCs so far reported were metastases from cutaneous sources. In the present article, we describe for the first time a primary gastric MCC harboring MCPyV. A 72-year-old man presented to clinical observation due to epigastric pain. Upper endoscopy revealed an ulcerated gastric tumor. The patient underwent total gastrectomy. The tumor was composed of mitotically active monomorphic small cells showing round nuclei with finely dispersed chromatin arranged in sheets and nests with large areas of necrosis. Tumor cells were positive for neuroendocrine markers and showed paranuclear dot immunoreactivity for cytokeratin 20. MCPyV was demonstrated with immunohistochemistry and electron microscopy, which showed intranuclear and intracytoplasmic viral particles. The MCPyV DNA in tumor cells was demonstrated with polymerase chain reaction analysis.