Congenital lobar emphysema is a rare disease and a cause of respiratory distress in early infancy. The most common location of pulmonary involvement is the left upper lobe. We diagnosed a case of congenital lobar emphysema in a 5-month-old female infant, who had a complex heart disease using flexible bronchoscopy. In spite of palliative heart surgery, respiratory difficulty and cyanosis did not improve and weaning from artificial ventilation was not possible. Chest X-ray and CT scan showed persistent hyperinflation in the left upper lobe. So, we performed flexible bronchoscopy. The findings showed no cartilage and patent bronchus during inspiration, but complete collapse during expiration due to a check valve effect in the left upper lobar bronchus. After excision of the involved lobe, the patient improved from respiratory distress. The observed airway patency during inspiration, and dynamic airway collapse on expiration suggest that bronchomalacia contributed to lung overinflation in this case.