Background Recently, bronchoscopy has been widely used to aid microbiological diagnosis in patients with little sputum. However, the usefulness of bronchoscopy and the patient groups that benefit from subsequent microbiological confirmation have not been established. Methods We retrospectively analyzed the data of the Korean tuberculosis (TB) cohort, a nationwide prospective observation cohort including patients with TB, from September 2018 to October 2019 to evaluate the usefulness of bronchoscopy in patients with microbiologically negative (based on initial sputum polymerase chain reaction and culture Results) pulmonary TB. The primary outcome was the proportion of microbiological diagnoses after bronchoscopy. The secondary outcomes were the predictors of microbiological confirmation and the percentage of additional resistance detection after bronchoscopy. Results A total of 5194 patients were diagnosed with pulmonary TB, and 937 patients were microbiologically negative based on initial sputum findings. Of them, 319 patients underwent bronchoscopy; further microbiological confirmation was checked in 157 (49.1%) patients. The predictors of microbiological confirmation after bronchoscopy were age >65 years, female sex, and low body mass index (BMI). The rate of additional resistance detection was 10.5% [Multidrug resistant (MDR)/Rifampin resistant (RR) 3.8%; Isoniazid resistant (Hr) 5.7%]. Conclusion Bronchoscopy was useful for detecting resistant pathogens. Bronchoscopy should be consider for microbiologically negative pulmonary TB with female, aged >65 years, and low BMI for subsequent microbiological confirmation.