A 61-year-old woman presented with solitary lymphadenopathy suspicious for lymphoma. An excisional biopsy of a right inguinal lymph node demonstrated metastatic Merkel cell carcinoma (MCC). No skin lesions were detected, but a primary nasopharyngeal mass was identified. A microscopic examination of the nasopharyngeal tumor and the lymph node metastasis showed a monotonous population of small- to intermediate-sized, round blue cells with vesicular nuclei, finely granular and dusty chromatin, and multiple nucleoli. Immunohistochemistry showed perinuclear dot-like staining for cytokeratins AE1/AE3 and CK20. Microscopic appearance and immunohistochemical stains were consistent with MCC. MCC was recently shown to harbor a novel polyomavirus, Merkel cell polyomavirus (MCPyV), in the majority of cases. In this case, MCPyV was detected in the primary tumor and metastasis using polymerase chain reaction and CM2B4 immunohistochemical stain. This is the first report to demonstrate the presence of MCPyV and CM2B4 in a mucosal MCC and its metastasis.