The present study describes two cases in which intraoperative thrombectomy was performed for occluded or severely stenosed carotid arteries in patients with acute aortic dissection complicated by cerebral malperfusion. A Fogarty catheter was inserted into the true lumen of the occluded branch under hypothermic circulatory arrest, and thrombi within the false lumen were removed. The arch vessels were patent on subsequent computed tomographic imaging, and no neurological complications were found postoperatively. In these cases, the choice of appropriate management strategies took into consideration the brain ischemic time and the presence or absence of cerebral infarction. This technique represents a useful option for the management of this clinical scenario.