Previous studies have reported that the extracardiac Fontan procedure has excellent outcomes and a lower incidence of postoperative complications than the lateral tunnel procedure. However, thromboembolic events that occur after the Fontan procedure are a well-known cause of morbidity. We experienced a case of thrombosis of intra-atrial extracardiac conduit and the left pulmonary artery 2 years after a modified Fontan operation due to infective endocarditis (IE) despite prophylactic antiplatelet therapy. The patient underwent reoperation. The conduit in the right atrium (RA) was excised, and the thrombus in the vessels was removed. Because the fibrous tissue in the RA around the conduit was firm, the tissue was used as the "tunnel" for the Fontan route between the IVC and the ePTFE graft outside the RA instead of replacement using another alien graft. He was discharged on postoperative day 45 and was medicated with coumadin and aspirin. He is now being followed in our outpatient clinic and is still without any sign of infection.