Primary calcitonin-secreting neuroendocrine carcinoma of the larynx is a rare neuroectodermal neoplasm currently classified as moderately differentiated (atypical carcinoid/WHO classification) neuroendocrine carcinoma of the larynx. Due to the rarity of these tumors at this location as well as their distinctive histologic and immunophenotypic features, they often raise significant diagnostic difficulties in biopsy specimens. We present a 57-year-old woman with persistent and gradually worsening pharyngeal pain for approximately one year duration, who was found to have a lesion limited to the right aryepiglottic fold. Final pathology showed moderately differentiated neuroendocrine carcinoma. Due to calcitonin positivity and coexistence of a thyroid nodule, the tumor raised the differential diagnosis of medullary thyroid carcinoma. A practical approach to pathologic diagnosis of laryngeal neuroendocrine tumors and discussion of clinical management is provided.