Endobronchial ultrasound-transbronchial needle aspiration (EBUS-TBNA) is a useful and safe diagnostic test. We herein report a case of endotracheal granuloma formation that occurred after EBUS-TBNA in a 73-year-old woman. The patient was admitted due to coughing and dyspnea after 70 days of antituberculous therapy for mediastinal lymphadenitis. Computed tomography revealed decreases in the size of the lymph nodes with a new mass protruding into the tracheal lumen. The mass originated from the right paratracheal area, which was a previous puncture site. This case suggests that clinicians should pay attention to complications because tuberculosis can produce new granulomas via the sinus tract after EBUS-TBNA.