Maternal smoking during pregnancy is significantly associated with complex congenital anomaly. Usually, mothers quit smoking as soon as they learn that they are pregnant to prevent harmful effects on the fetus. We report a 9-day-old boy found to have critical coarctation of the aorta (CoA) with severe left ventricular (LV) dysfunction and perinatal stroke who was born to a mother with a history of heavy smoking before, during pregnancy, and after birth. Initial echocardiography revealed a discrete CoA with a pressure gradient of 35 mmHg and severe LV dysfunction (LVEF, 32%). Initial treatment was started with prostaglandin E1 and mechanical ventilation. On hospital day 1, balloon aortic angioplasty was immediately performed at coarcted segment. After the procedure, the coarcted segment increased in diameter and the initial pressure gradient of 35 mmHg disappeared completely with remarkably improved the LV dysfunction. On hospital day 2, he showed sudden seizure-like movements in the morning, brain computed tomography findings suggested a suspicious infarction. And brain magnetic resonance imaging revealed infarction with hemorrhagic transformation at the left middle cerebral artery territory, which was thought to have developed at the age of 2–3 days. We initiated administration of phenobarbital and low-dose aspirin. Follow-up echocardiography revealed improved LV function (LVEF, 79%), but an increase in pressure gradient across the isthmus to 25 mmHg finally confirmed the need for operation. Thereafter, coarctectomy and aortic arch repair was successfully performed without any complications. This staged treatment is a good option for this case. Furthermore, maternal smoking is associated with a significantly higher risk of thromboembolism associated with perinatal stroke. In this case, the patient had some high risk factors of perinatal stroke, including heavy maternal smoking. Additionally, procedure such as aortic balloon angioplasty likely cause thromboembolism during procedure. Therefore, considering that neonates with CHD who are born to mothers who smoke during pregnancy are already at high risk, we suggest that these neonates undergo screening for perinatal stroke by using brain imaging. Second, anticoagulation should be started to prevent newly developed thrombosis during catheterization in cases such as that reported herein.