We report here on a case of congenital Klippel-Trenaunay syndrome with vascular abnormalities in the central nervous system. A 15-year-old male patient was hospitalized for headache. The neurological examination revealed that the patient was physiognomically sluggish and unresponsive. A general examination found that the right upper arm and the left lower leg of the patient displayed hemihyperplasia and wine-colored spots. A CT scan identified multiple patches of high density shadows in the left cerebellar hemisphere and the left temporo-occipital lobe. Larger shadows were found in the left cerebellum, which had a region of low-density edema surrounding it. The right transverse sinus and the sigmoid sinus were dilated, with dilation of the sigmoid sinus more obvious than that of the transverse sinus. Moreover, density was increased in the sigmoid sinus. An MRI of the brain also showed that the right straight sinus and the sigmoid sinus were dilated. A brain MRA revealed large areas of patchy, high signal shadows in the right straight sinus. Following treatment, the patient was discharged after his symptoms subsided. Congenital Klippel-Trenaunay syndrome with vascular abnormalities in the central nervous system is rare, and the treatment of vascular malformations in the nervous system is difficult.