Congenital bronchial atresia is a rare airway malformation in which a segmental or lobar bronchus is isolated from the main airway, and corresponding lung tissue is hyperinflated via collateral pathways and becomes emphysematous. We reported a young man with congenital bronchial atresia who presented with chronic cough with a borderline restriction of pulmonary function, and was treated successfully with thoracoscopic tri-segmentectomy. Possible differential diagnoses were also discussed.