We report acute thromboembolic events in a 14-year-old boy with Down syndrome and repaired atrioventricular septal defect. He presented with sudden onset of bilateral lower limb ischemia. Transesophageal echocardiography detected a thrombus in the right atrium. An arterial saddle embolus was removed following bilateral iliac embolectomy. Despite anticoagulation, he presented again with sudden bilateral lower limb ischemia and respiratory distress. Multiple pulmonary emboli and a thrombus in the right atrium were noted on imaging studies. An arterial embolus was removed from the abdominal aorta at the bifurcation. To our knowledge, this is the first report of a child or adolescent with a repaired congenital heart lesion and arterial embolism requiring embolectomy. This association and possible etiological factors are discussed.