Abstract. Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is of limited usefulness for diagnosing thyroid disease, and few studies have reported its use in diagnosing and treating thyroid cysts. The present study investigated a unique case of diagnosis and treatment of a thyroid cyst by EBUS-TBNA. A 67-year-old male presented with back pain. Positron emission tomography/computed tomography scanning revealed low-density signals in the right lobe of the thyroid. Needle aspiration biopsies and drainage at this site was performed, and EBUS was used for guidance in diagnosing the thyroid cyst. A follow-up chest computed tomography scan indicated that the thyroid lesion had subsequently disappeared. The present study concludes that EBUS-TBNA provides an alternative approach for diagnosing and treating deep thyroid cysts located close to the airway. In all other cases, percutaneous needle aspiration or surgery should be the first choice.