We herein report a rare case of a newborn girl with a right-sided congenital diaphragmatic hernia where a herniated liver had an abnormal vessel communication with the right lung. A surgical repair was initially attempted through a thoracic approach at 4 days of age where only a plication of the hernia capsule was performed without a prominent improvement in the respiratory condition. At 1 year of age, an angiographic examination was performed, which revealed pulmonary hypertension and abnormal vessel communications where the right pulmonary flow returned to the herniated liver and the right lung also received an arterial supply from the liver. During the second surgical repair performed at 1 year and 1 month of age, an abdominal approach through a right subcostal incision was selected. The aberrant vessels between the lung and the liver were carefully identified and ligated. Because the right lobe of the liver was completely herniated, a hepatic segmentectomy of S6 and S7 was performed. The patient has been doing well for 21 months without any mechanical ventilation since 2 months after undergoing the radical second operation. When performing surgery on a right-sided diaphragmatic hernia, the potential presence of such a vessel anomaly should be carefully taken into consideration.