We report a 54-year-old woman who presented with a well-defined, homogeneous, and non-enhancing mass in the retrobronchial region of the bronchus intermedius. The patient underwent endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) for histological confirmation. Serous fluid was aspirated by EBUS-TBNA. Cytological examination identified an acellular smear with negative microbiological cultures. The patient was finally diagnosed with bronchogenic cysts by chest computed tomography (CT) and EBUS-TBNA findings. However, 1 week after EBUS-TBNA, the patient developed bronchogenic cyst rupture and pneumonia. Empirical antibiotics were administered, and pneumonia from the bronchogenic cyst rupture had resolved on follow-up chest CT. To our knowledge, this is the first reported case of pneumonia from bronchogenic cyst rupture after EBUS-TBNA.