Small cell neuroendocrine carcinoma (NEC) of the tongue is an extremely rare entity with only seven cases reported in literature till date. These are high-grade tumors with a dismal prognosis. There is much ambiguity regarding the classification, treatment protocols and prognostic factors of these tumors due to the paucity of studies. We describe an exceptionally rare and unusual case of small cell NEC of the base of tongue arising in an elderly man 6 years after receiving radiotherapy for the treatment of squamous cell carcinoma at the same site. The diagnosis was confirmed on histopathological examination and supported by immunohistochemical positivity for neuron-specific enolase, synaptophysin, chromogranin, pan-cytokeratin, and cytokeratin 7. To the best of our knowledge, this is the first case of intraoral NEC arising many years later within the irradiated field of the initial tumor.