ObjectiveThe present study assessed the diagnostic and prognostic significance of endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) for suspected intrathoracic metastasis after HNC treatment.MethodsA retrospective analysis was conducted on 75 patients with a prior history of head and neck cancer treatment who underwent EBUS‐TBNA for suspected intrathoracic metastases between March 2012 and December 2021.ResultsA total of 126 targeted lesions, including 107 mediastinal/hilar lymph nodes and 19 intrapulmonary/mediastinal masses, were sampled. The metastatic head and neck cancer (HNC) cases detected by EBUS‐TBNA consisted of nasopharyngeal carcinoma (n = 24), oropharyngeal carcinoma (n = 3), hypopharynx carcinoma (n = 6), laryngeal carcinoma (n = 6), and oral cavity carcinoma (n = 6). Cases with negative EBUS‐TBNA results consisted of tuberculosis (n = 9), sarcoidosis (n = 3), anthracosis (n = 9), and reactive lymphadenitis (n = 9). Six false‐negative cases were found among the 75 patients with suspected intrathoracic metastases. The diagnostic sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of the EBUS‐TBNA procedure for metastatic HNC were 88.2, 100.0, 100.0, 80, and 92.0%, respectively. The diagnosis of HNC intrathoracic metastasis by EBUS‐TBNA correlated with an adverse prognosis in terms of overall survival (OS) (P = .008). The log‐rank univariate analysis and Cox regression multivariate analysis results indicated that the detection of metastatic HNC through EBUS‐TBNA was a significant independent prognostic factor for patients with HNC who had received prior treatment.ConclusionsEndobronchial ultrasound‐guided transbronchial needle aspiration is a safe, effective, and minimally invasive procedure for assessing suspected intrathoracic metastasis in HNC patients after treatment. The intrathoracic metastasis detected by EBUS‐TBNA has crucial prognostic significance in previously treated HNC patients.