Early extubation appears to have beneficial effects on the Fontan circulation. The goal of this study was to assess the impact of extubation on the operating table in comparison with extubation during the first hours after Fontan operation (FO) on the early postoperative course. Between 2013 and 2016, 114 children with a single ventricle heart malformations (mean age, 3.8 ± 2.3 years) underwent FO: 60 patients were extubated in the operating room (ORE) and 54 in the intensive care unit (ICUE) in the median time of 195 min (range 30-515 min) after procedure. Pre-, peri-, and postoperative records were retrospectively analyzed. The hospital survival rate was 100%. One patient from the ORE group needed an immediate reintubation because of laryngospasm. The ORE group showed lower heart rate (106.5 vs. 120.3 bpm; p < 0.001) and lower central venous pressure (10.4 vs. 11.4 mmHg; p = 0.001) than patients in the ICUE group within the first 24 h after FO, as well as higher systolic blood pressure within 7 h after operation (88.6 ± 2.5 vs. 85.6 ± 2.6 mmHg; p = 0.036). The ORE children manifested significantly less pleural effusions during 48 h after FO (38.0 vs. 49.5 ml/kg; p = 0.004), received less intravenous fluid administration within 24 h after FO (54.1 vs. 73.8 ml/kg; p = 0.019), less inotropic support (9.8 vs. 12.8 h of dopamine; p = 0.033), and less antibiotics (4.7 vs. 5.8 days; p = 0.037). ICUE children manifested metabolic acidosis more frequently than the ORE group 3-4 h after FO (p < 0.05). Immediate extubation after FO in comparison with extubation in the ICU appears to be associated with improved hemodynamics and reduced application of therapeutic interventions in the postoperative course.