The optimum postoperative anticoagulation therapy type and duration after the Fontan procedure remains unclear. This study aimed to evaluate whether our approach of administering only oral antiplatelets without warfarin due to serious bleeding complication risks in children is reasonable. We retrospectively reviewed the data of 249 patients who underwent the Fontan procedure. Total cavopulmonary connection with extracardiac conduit was performed in 230 patients (92%), the lateral tunnel Fontan procedure was performed in 18 patients (8%), and intraatrial conduit Fontan procedure was performed in one patient. Aspirin administration (initial dose: 5 mg/kg/day) was continued in all patients. Only 29 patients (11%) received combined administration of aspirin and warfarin for various reasons, and warfarin was discontinued in 20 (71%) of these within a median of 16 months postoperatively. Sixteen patients at high risk of thromboembolism were started on warfarin. Hospital mortality was 0%, with no thromboembolic or bleeding event-related early death. Nine late deaths, not associated with bleeding nor thromboembolism, occurred except one resulting from cardiac infarction 1.9 years after the procedure. During hospitalization, five patients experienced graft thromboembolism, two of which underwent graft exchange, and the others were started on warfarin. In the late phase (3.1 ± 6.6 years), cerebral infarction (n = 3), peripheral pulmonary artery occlusion (n = 2), gastrointestinal bleeding (n = 5), and respiratory hemorrhage (n = 4) occurred. Eight of nine patients with bleeding events received only aspirin. Thromboembolic events occurred in six patients within the first year after the procedure. Bleeding events occurred at 8 ± 5.5 years after the procedure. Expected freedom from a thromboembolic event was 99.8% at 1 year and 93.4% at 20 years. Expected freedom from a bleeding event was 100% at 1 year and 88.4% at 20 years. In children at low risk of thromboembolism after the Fontan procedure, continuous administration of an oral antiplatelet agent alone without warfarin seems to represent a reasonable prophylactic approach.