Atrio-esophageal fistula (AEF) is one of the most devastating complication of radiofrequency catheter ablation (RFCA) of atrial fibrillation (AF) and surgical repair is strongly recommended. However, optimal surgical approach remains to be elucidated. We retrospectively reviewed AEF cases that occurred after RFCA in a single center and evaluated the clinical results of different surgical approach. Surgical or endoscopic repair was attempted in five AF patients who underwent RFCA. Atrio-esophageal fistula and mediastinal infection was not controlled in the patient who underwent endoscopic repair eventually died. Lethal cerebral air embolism occurred two days after surgery in a patient who underwent esophageal repair only. Primary surgical repair of both the left atrium (LA) and esophagus was performed in the remaining three patients. Among these three patients, two underwent external LA repair and the remaining had internal LA repair via open-heart surgery. External repair of the LA was unsuccessful and one patient dies and another had to undergo second operation with internal repair of the LA. The patient who underwent internal LA repair during the first operation survived without additional surgery. Furthermore, we applied veno-arterial extracorporeal membrane oxygenation (VA-ECMO) with artificial induction of ventricular fibrillation in this patient to prevent air and septic embolism and she had no neurologic sequelae. In summary, surgical correction can be considered preferentially to correct AEF. Open-heart surgical repair of LA from the internal side seems to be an acceptable surgical method. Application of VA-ECMO with artificial induction of ventricular fibrillation might be effective to prevent air and septic embolism.