Real-time endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) with a dedicated EBUS bronchoscope has been reported as a minimally invasive and accurate method for sampling specimens from mediastinal and hilar lesions. Using this method, not only cytologic but also histologic specimens, which provide valuable information for a definitive diagnosis, can often be obtained. We report a case of an enlarged metastatic mediastinal lymph node from an unidentified primary papillary thyroid carcinoma that was accurately diagnosed by histological and immunohistochemical examination of tissue obtained by EBUS-TBNA.