The benefit of additional pulmonary blood flow (APBF) in Fontan pathway remains controversial. The aim of the study was to analyze the systemic arterial saturation, ventricular and atrioventricular (AV) valve function, development of pulmonary arteries and postoperative course after Fontan operation in children with preserved or eliminated APBF between stages 2 and 3 of the Fontan pathway. A group of 180 consecutive children (median age: 2.92(1.83-16.83) years) with single ventricle underwent extracardiac conduit Fontan operation. The patients were retrospectively analyzed with respect to the presence of APBF between stages 2 and 3. Preoperative echocardiography showed no differences in ventricular function (good - 105[95%] vs. 65[98.5%]; reduced - 9[5%] vs 1[1.5%]; p = 0.07) or AV valve function (p = 0.78). There was no difference in oxygen saturation at admission (p = 0.48), in preoperative blood gas analysis (p = 0.62), or at the discharge (p = 0.73). There was no difference in size of the left pulmonary artery (9.5(0-16.2) vs 10.6 (4.9-21.7) mm; p = 0.13), however the right pulmonary artery was significantly larger (11.2(6.5-19.6) vs. 12.8(7.8-2.5) mm; p = 0.048) in APBF group. In this group the mean pressure in the pulmonary artery was significantly higher as well (8[4-17.5] vs 9.5[4-17.3] mmHg; p = 0.03). APBF does not result in higher oxygen saturation, both before and after Fontan completion. APBF can stimulate the growth of the pulmonary arteries and increase the pulmonary artery pressure. The presence of APBF does not affect the post-operative course after Fontan operation, however it can increase the need of AV valve reconstruction.