A 53-year-old man with a history of dyspepsia and Helicobacter pylori infection, underwent months of medication therapy. A persistent lumping sensation in his throat for over six months led him to an otolaryngologist's examination, which revealed a 1 cm cystic tumor in the hypopharynx near the esophageal opening. The symptoms and tumor size did not respond to the medication, necessitating surgical removal via microlaryngoscopy. The symptoms resolved postoperatively, and the histopathology confirmed a tonsillar cyst. Tonsillar cysts, akin to lymphoepithelial cysts, commonly occur in the oropharyngeal tonsillar tissue. While often symptomless when small, they can cause a lump sensation when enlarged, especially in sensitive areas like the lower pharynx. Some experts suggest their origin from branchial arch tissue due to histological similarities with branchial cysts. The etiology, possibly linked to abundant lymphoid tissue or chronic pharyngitis, requires further investigation. Despite the tumor's modest size, its location underscores the need for prompt diagnosis and surgical intervention, highlighting the ongoing quest to understand its mechanisms. (J Taiwan Otolaryngol Head Neck Surg 2024; 59:34-39)