We describe total arch replacement after ascending aortic replacement for acute type II dissecting aneurysm with associated anomaly of the left vertebral artery. A female patient was recommended at 10 years of age after the initial operation because of an enlargement of the distal ascending aorta. Magnetic resonance angiography revealed an isolated left vertebral artery that arises distal to the left subclavian artery. Total arch replacement was proceeding using selective cerebral perfusion. The isolated artery was reconstructed with a saphenous vein graft interposed between the native left vertebral artery and the side of the graft branch anastomosed to the left subclavian artery. The patient recovered uneventfully after extensive surgical replacement of the thoracic aorta and remains asymptomatic at 1 year after the procedure. To prevent possible neurological complications, we find it critical to assess vascularization in this region prior to conducting surgical procedure. Careful examination and correct identification of the vessels are essential to avoid major complications.