Acute type A aortic dissection (ATAAD) is a surgical emergency with a mortality of 1–2% per hour. Since its discovery over 200 years ago, surgical techniques for repairing a dissected aorta have evolved, and with the introduction of hypothermic circulatory arrest and cerebral perfusion, complex techniques for replacing the entire aortic arch were possible. However, postoperative neurological complications contribute significantly to mortality in this group of patients. The aim of this study was to determine the association between different bilateral selective antegrade cerebral perfusion (ACP) times and the incidence of postoperative ischemic stroke in patients with emergency surgery for ATAAD. Patients with documented hemorrhagic or ischemic stroke, clinical signs of stroke or neurological dysfunction prior to surgery, that died on the operating table or within 48 h after surgery, from whom the postoperative neurological status could not be assessed, and with incomplete medical records were excluded from this study. The diagnosis of postoperative stroke was made using head computed tomography imaging (CT) when clinical suspicion was raised by a neurologist in the immediate postoperative period. For selective bilateral antegrade cerebral perfusion, we used two balloon-tipped cannulas inserted under direct vision into the innominate artery and the left common carotid artery. Each cannula is connected to a separate pump with an independent pressure line. Near-infrared spectroscopy was used in all cases for cerebral oxygenation monitoring. The circulatory arrest was initiated after reaching a target core temperature of 25–28 °C. In total, 129 patients were included in this study. The incidence of postoperative ischemic stroke documented on a head CT was 24.8% (31 patients), and postoperative death was 20.9% (27 patients). The most common surgical technique performed was supravalvular ascending aorta and Hemiarch replacement with a Dacron graft in 69.8% (90 patients). The mean cardiopulmonary bypass time was 210 +/− 56.874 min, the mean aortic cross-clamp time was 114.775 +/− 34.602 min, and the mean cerebral perfusion time was 37.837 +/− 18.243 min. Using logistic regression, selective ACP of more than 40 min was independently associated with postoperative ischemic stroke (OR = 3.589; 95%CI = 1.418–9.085; p = 0.007). Considering the high incidence of postoperative stroke in our study population, we concluded that bilateral selective ACP should be used with caution, especially in patients with severely calcified ascending aorta and/or aortic arch and supra-aortic vessels. All efforts should be made to minimize the duration of circulatory arrest when using bilateral selective ACP with a target of less than 30 min, in hypothermia, at a body temperature of 25–28 °C.