Sequential atrioventricular activation plays a critical role in the physiology of Fontan circulation. Although bradycardia is usually well tolerated, retroconducted junctional rhythm may acutely increase atrial pressure impairing cardiac output. Echocardiographic evaluation can reveal clues of this hemodynamic condition. The clinical impact of arrhythmic disturbance on the follow up of patients who had undergone total cavo-pulmonary connection is well recognized but the role of transient periods of retroconducted junctional rhythm on the immediate post-operative course is less defined. We describe two cases of acute Fontan circulatory failure due to postoperative retroconducted escaping junctional rhythm despite an adequate heart rate and circadian variation. The patients rapidly improved after atrial pacing, allowing discharge with a minimal dose of diuretic.