Thromboembolic complications occur frequently in Fontan patients with atrial arrhythmias and are a cause of significant morbidity and all-cause mortality. We report the case of an adult woman with direct atriopulmonary connection and atrial arrhythmia who developed a right atrial thrombus. She was switched to apixaban therapy because of echocardiographic evidence of thrombus progression despite combined therapy with warfarin and aspirin. After 1 year of treatment, there was evidence of complete thrombus resolution, in the absence of bleeding events. Our case shows that direct oral anticoagulants can be effective and safe for the treatment of thrombosis in adult patients with complex CHD.