There are no clear guidelines on thromboprophylaxis in patients following Fontan surgery. In addition, most reports on thromboprophylaxis refer to systemic thromboembolism. Therefore, there are few reports on thromboprophylaxis for extracardiac conduits. We experienced a case of thrombus in extracardiac conduit leading to liver damage after the Fontan completion. The patient was an 11-year-old girl, who underwent the Fontan procedure at 3 years of age. She was on aspirin for thromboprophylaxis. Eight years postoperatively, cardiac catheterization demonstrated severe conduit stenosis, and chronic liver damage was seen at that time. The patient successfully underwent conduit replacement. Subsequently, ascites disappeared and platelet count improved. Conduit stenosis after Fontan completion is a rare but serious complication, therefore we should always keep it in mind and aspire to early detection.