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An octogenarian woman with Merkel cell carcinoma of the right upper arm, staged as Stage IIIA at initial diagnosis, underwent wide local excision with sentinel lymph node biopsy followed by adjuvant radiation therapy. She later developed regional nodal recurrence requiring axillary dissection, which was confirmed by biopsy as metastatic Merkel cell carcinoma, requiring axillary dissection. Despite subsequent treatment with pembrolizumab, she developed progressive metastatic disease one year later, with new hepatic and pulmonary lesions. Biopsy of a hepatic lesion demonstrated a poorly differentiated neuroendocrine carcinoma with a high proliferative index. Notably, immunohistochemistry showed absence of cytokeratin 20 (CK20) expression, raising diagnostic uncertainty regarding lineage confirmation in the setting of CK20-negative metastatic disease. Given the clinical context, the patient was treated with carboplatin and etoposide per established guidelines for high-grade neuroendocrine tumors; however, she exhibited continued disease progression and ultimately transitioned to hospice care, where she died. This case highlights the diagnostic and therapeutic challenges of advanced Merkel cell carcinoma in the setting of immune checkpoint inhibitor exposure, particularly the potential for loss of the canonical Merkel cell carcinoma immunophenotype at metastatic sites following such therapy. It underscores the importance of integrating clinical history, treatment exposure, and morphologic findings when evaluating atypical metastatic neuroendocrine neoplasms, especially when canonical immunohistochemical markers such as CK20 are absent.