Arteriopathy of the central nervous system (CNS) complicated with ulcerative colitis is a rare condition, moreover the involvement of extracranial arteries has not been documented. An 18-year-old female complained of a severe pulsatile headache and nausea. She had been diagnosed and treated for ulcerative colitis for four years. Magnetic resonance imaging of the brain showed normal results; however, magnetic resonance angiography (MRA) revealed severe irregularity of the intracerebral arteries. After treatment with prednisolone, the patient fully recovered and the irregularity of the intracerebral arteries was dramatically improved. Vasculitis was strongly suggested as the cause of arteriopathy of the CNS in the present case. Involvement of extracranial arteries such as the carotid artery was also incidentally discovered by duplex ultrasonography and the HLA typing suggested genetic susceptibility to Takayasu's arteritis. Findings from our patient suggest that extracranial arterial involvement should be considered in the case of arteriopathy of the CNS associated with ulcerative colitis.