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Background: Clinical characteristics of endobronchial tuberculosis (EBTB) patients whose sputum smears were negative have not been elucidated yet. Method: EBTB patients with negative sputum smears were documented retrospectively at the outpatient pulmonary clinic from late 2015 to early 2019. Results: We described the characteristics of 31 EBTB patients with negative sputum smears. The median age was 36 years (range 18–81 years). The male-to-female ratio is 1:1.58. The “peripheral” lesion group included 16 cases with opacity/consolidation, 2 cases with atelectasis, 1 case with cavitary lesion, and 1 case with pleural effusion. The “central” lesion group included four cases with normal chest X-ray and seven cases with only unilateral hilar enlargement. EBTB patients with “central” lesion were more common the presence of cough, the positive rate of bronchial lavage acid-fast bacilli smear, and the rate of misdiagnosis as pharyngitis, bronchitis, or asthma than that with “peripheral” lesion. Conclusions: EBTB with negative sputum smears was found in adult patients at any age and predominant in females. The diagnosis of EBTB with “central” lesion was more difficult than that with “peripheral” lesion. The location of the lesion could play a role in inducing cough among EBTB patients.