A 3-year-old boy underwent surgical closure of a large ostium secundum atrial septal defect. This was complicated with extensive right atrial thrombus formation and pulmonary thromboembolism immediately following surgery. He was managed with emergency surgical thromboembolectomy and anticoagulation. However, new thrombus was formed again immediately. This prompted us to add thrombolysis to his treatment, but with no effect. He died on the fifth postoperative day. A postmortem study confirmed extensive thromboembolism.