A 57-day-old boy, with prenatal echocardiography indicating pulmonary atresia with intact ventricular septum, developed cyanosis of the lips about 8 h after birth. The prenatal echocardiography indicated pulmonary atresia with intact ventricular septum (PA/IVS). He was admitted to our hospital because of acute exacerbation of cyanosis for 2 days. Wheezing respiration and severe cyanosis of the lips were observed. The blood pressure (BP) was 46/30 mm Hg, and the pulse oxygen saturation (SpO2) was 45%. Immediate endotracheal intubation and mechanical ventilation were conducted. Dopamine at 5.0 μg/(kg·min) was intravenously administered to enhance cardiac function along with prostaglandin E1 at 5.0 ng/(kg·min) to maintain the ductus arteriosus patency. However, the patient’s BP and SpO2 could not be maintained, and the lactate level continuously increased, which could not be alleviated by adjustment of drug dosages. Therefore, he was scheduled to undergo an emergency B-T shunt surgery under general anesthesia. This article introduced the key points of anesthetic management of emergency B-T shunt surgery in an infant with PA/IVS.