Background <p>Lingual thyroglossal duct cysts (LTGDCs) are an exceedingly rare subset of congenital cervical anomalies, accounting for a small proportion of thyroglossal duct cysts. Their deep-seated location at the tongue base often leads to delayed diagnosis and presents risks such as dysphagia, airway obstruction, and speech impairment.</p> Case presentation <p>We report the case of a 13-year-old boy with a gradually enlarging mass at the base of the tongue, first noticed at the age of six. The patient presented with progressive dysphagia in the absence of respiratory symptoms. Clinical and nasofibroscopic examination revealed a well-defined lesion on the left side of the tongue base. Magnetic resonance imaging confirmed a cystic lesion consistent with a thyroglossal duct cyst, while thyroid ultrasound showed a normally positioned and functioning gland. Surgical excision was performed via an external transhyoid Sistrunk approach, ensuring complete removal without pharyngotomy. Postoperatively, the patient developed a minor serous collection managed conservatively. Histopathological analysis confirmed a benign thyroglossal duct cyst.</p> Conclusion <p>LTGDCs are rare and often overlooked congenital anomalies that require high clinical suspicion, appropriate imaging, and tailored surgical management. The transhyoid Sistrunk procedure remains the gold standard for complete excision, offering low recurrence rates and favourable functional outcomes. This case highlights the diagnostic and therapeutic challenges posed by LTGDCs and underscores the importance of an anatomy-guided, multidisciplinary approach in paediatric neck masses.</p>