Merkel cell carcinoma (MCC) is a rare and aggressive cutaneous neuroendocrine neoplasia. Surgical resection is the first-line therapeutic option, and radiation therapy is an alternative treatment for inoperable cases. Herein, we report a case of primary MCC (cT2N0M0, stage IIA) of the head and neck region. This case was misdiagnosed as a metastatic tumor and referred to the department of radiation oncology for palliative irradiation. Additional immunohistochemical analysis confirmed the diagnosis of MCC, and the tumor was treated with definitive radiation therapy (66 Gy in 33 fractions), leading to complete in-field control. This case indicates that even in patients with suspected metastatic tumors referred for palliative treatment, patient characteristics and pathology should be carefully examined to avoid missing potentially controllable primary tumors. In such cases, MCC, although rare, should be included in the differential diagnosis of head and neck lesions.