A newborn female was transferred to our hospital presenting with severe respiratory distress. She underwent tracheal intubation and nasogastric tubing. Investigations revealed a congenital extrahepatic portosystemic shunt (CEPS) type 1, biliary atresia, heterotaxia, polysplenia, malrotation and a double aortic arch (DAA). She underwent the Kasai portoenterostomy and the Ladd procedure when she was 29 days old. On postoperative day 20, she developed sudden hematemesis with bright red blood. Endoscopy showed massive bleeding from an esophageal ulcer, and endoscopic therapy was performed successfully. During left thoracotomy, an aortoesophageal fistula (AEF) was detected and repaired by direct suturing. The postoperative course was uneventful. CEPS type 1 is commonly associated with other congenital malformations; however, there have been no previous reports of an association between CEPS and DAA. Nasogastric tube insertion in a patient with DAA can result in catastrophic AEF. The treatment strategy should be carefully considered in patients with CEPS type 1 and multiple congenital fetal anomalies.