The goal of the study was to compare the early postoperative course after fenestrated lateral atrial tunnel (LT) and non-fenestrated extracardiac conduit (EC) Fontan operation (FO) in a single center where both techniques were parallelly used. Between 2004 and 2012, 56(32.7%) children underwent LT and 113(66.1%) EC FO. The mean age was 3.7 ± 2.9 years and mean weight was 14.6 ± 7.3 kg. The most common malformation was hypoplastic left heart syndrome (50.9%). The general approach was to perform LT in children after hemi-Fontan operation and EC in patients after Glenn anastomosis. Medical records were retrospectively reviewed. The hospital survival was 100%. In EC group, cardiopulmonary bypass time (CPB) was shorter (p = 0.004) and less patients needed aortic cross-clamping (p < 0.001). Children after EC stayed longer in the hospital (p = 0.016) and manifested more often prolonged effusions (p = 0.038). The incidence of all forms of junctional rhythm was higher in the LT group, early postoperatively (p < 0.001), during hospitalization (p = 0.004) and at discharge (p < 0.001). Children after LT required more often temporary pacemaker stimulation (p < 0.001). Patients without postoperative normofrequent sinus rhythm had longer CPB time (p = 0.008) and were more often operated on with aortic cross-clamping (p = 0.028). Lateral atrial tunnel Fontan operation with fenestration facilitates early adaptation to the total passive pulmonary flow, but predisposes the patients to the loss of sinus rhythm. The crucial role in the preservation of sinus rhythm plays the last step of the multistage surgery of the single ventricle malformations, probably not only the surgical technique but also factors associated with the cardiopulmonary bypass.