Pulmonary atresia with intact ventricular septum (PAIVS) is sometimes associated with coronary artery anomalies, including right ventricle (RV)-to-coronary artery fistulas (sinusoidal communications), coronary artery stenoses, and coronary artery occlusions. In some cases, the coronary circulation depends entirely or partly on the desaturated systemic venous blood supply from the RV. Under these circumstances, decompression of the RV can result in fatal myocardial ischemia. A 6-month-old boy, diagnosed with PAIVS associated with sinusoidal communications, underwent a bidirectional cavopulmonary shunt procedure under venoarterial cardiopulmonary bypass (CPB). During CPB, to prevent RV decompression, we maintained right atrial pressure above 5 mmHg and used a pump perfusion rate of 30%-40% of the calculated value based on body surface area. Although electrocardiography showed slight ST depression and bradycardia, myocardial contractility after weaning from CPB was adequate to maintain the circulation with the administration of dobutamine and atrial pacing. In patients with PAIVS and RV-dependent coronary circulation, it is important to maintain coronary artery perfusion throughout the period of anesthesia.