A shaggy aorta with a mobile atheromatous plaque in a thoracic lesion is considered a risk factor for cerebral infarction during aortic arch surgery. The brain isolation technique was introduced to prevent embolic stroke either by manipulating the severely atheromatous aorta, or by producing a sandblasting effect using the arterial jet in cardiopulmonary bypass. We performed total arch replacement with the aid of a brain isolation technique in four patients with aortic arch aneurysm complicated with a shaggy aorta between 2016 and 2020. Antegrade selective cerebral perfusion was established prior to systemic perfusion of the cardiopulmonary bypass. Total arch replacement using the frozen elephant technique was performed in all patients. There was no operative mortality, and all patients were discharged without major neurological complications. Therefore, the brain isolation technique could be a useful adjunctive method to prevent embolic stroke in patients who undergo total arch replacement for aortic arch aneurysm with a shaggy aorta.