Pulmonary embolism is an uncommon but potentially fatal disease in children, especially with congenital heart disease where pulmonary perfusion depends on caval flow. Anticoagulation is the mainstay of therapy for children with pulmonary embolism. However, thrombolytic therapy can also be considered. The outcome of pediatric pulmonary embolism is uncertain and needs further investigation. We suggest increased awareness and a high index of suspicion in the presence of suggestive clinical signs in high-risk patients in order to initiate prompt diagnostic imaging and treatment.