In this report, we present a case of intracranial thrombus migration that contributed to the postoperative exacerbation of neurological injury in a 69-year-old man with acute type A aortic dissection complicated by cerebral malperfusion. Our findings underscore perioperative thrombus migration as a potentially underrecognized factor influencing inconsistent surgical outcomes. A comprehensive perioperative evaluation, including a detailed assessment of intracranial arteries, is imperative.