A 19-year-old man presented with persistent cough and fever, raising the possibility of pneumonia, and the symptoms improved with antibiotics. However, one week later, an abnormal shadow was noted in the right hilum, and he was referred to our department. Chest CT showed no continuity between the right B1 and central bronchus, and the interrupted B1 root communicated with a cystic lesion, 4.8 × 3.8 cm in size, with niveau located on the dorsal side of the tracheal bifurcation. In addition, V1+2+3 flowed into the superior vena cava. The mass was diagnosed as bronchial atresia in communication with a mediastinal cyst with partial anomalous pulmonary venous return. The upper right lobe of the lung and mediastinal cyst were resected in a single mass because of repeated pneumonia considered to be caused by bronchial atresia. The diagnoses of mediastinal cyst and bronchial communication were confirmed on examination of the excised specimen, and the cyst was histopathologically diagnosed as an esophageal cyst. We report a rare surgical case of congenital bronchial atresia with an esophageal cyst and partial anomalous pulmonary venous return.