Thrombus formation can be a significant cause for morbidity and mortality after Fontan operation. Intracardiac thrombus formation can lead to chronic pulmonary embolic disease if formed on the right side, or stroke, if on the left side of the heart. Right-sided embolism may result in ventilation/perfusion mismatch or elevation of pulmonary vascular resistance, both of which may seriously hamper cavopulmonary physiology. We report the case of a 22-year-old patient, with past history of classic Fontan procedure performed at the age of six to palliate a single-ventricle tricuspid atresia, who presented with a massive pulmonary embolism and hemodynamic instability. Due to his critical status, mechanical fragmentation of the clot using the angiography catheter was started, followed by a local catheter-directed infusion of urokinase. This case demonstrated that pharmacomechanical thrombolysis therapy with a standard Pig-tail catheter and thrombolytic therapy with urokinase is secure, effective, and appropriated to manage heart chamber and pulmonary arterial thrombosis in patients with congenital heart disease.