A case of a 4-month-old child with an aortopulmonary fenestration weighing 6.6 kg who underwent successful transthoracic minimally invasive occlusion in our hospital was reported in this article. The child was transferred from the intensive care unit (ICU) to the general ward 1 day after surgery and discharged 5 days later. Compared with conventional ligation or repair of extracorporeal circulation for the aortopulmonary fenestration, the transthoracic minimally invasive occlusion is characterized by less trauma and faster recovery. However, it requires strict surgical indications and is not suitable for all patients with aortopulmonary fenestration.