Squamous cell carcinoma is the most predominant type of malignancy in the head and neck region with neuroendocrine carcinomas (NECs) being a rare occurrence. Here we report a rare case of small cell non-keratinizing NEC (WHO grade 3), TNM (tumor, node, and metastasis) stage T3N1M0, involving the larynx and the base of the tongue, in a 54-year-old male patient, demonstrating its rarity in an uncommon anatomical site and an aggressive and relatively uncommon pattern of spread for this tumor, over a period of two months. NECs in the head and neck region, especially those affecting the larynx and the posterior third of the tongue, remain exceedingly rare, comprising only a small fraction of malignancies in this region. The aggressive nature and distinct pattern of spread observed in this case underscore the importance of recognizing such unusual presentations for appropriate diagnosis and management. Given the rarity of this tumor type, a comprehensive understanding of its clinicopathological features is essential for guiding effective treatment strategies. We also discuss the treatment.