The authors report a case of a patient with Down syndrome in whom the abnormal course of the right vertebral artery (VA) at the craniovertebral junction (CVJ) was accurately demonstrated on three-dimensional (3D) computerized tomography (CT) angiography. The patient was a 5-year-old boy, who developed severe myelopathy. Bone abnormalities were also present at the CVJ, including atlantoaxial and occipitoatlantal instabilities, a hypoplastic odontoid process, and ossiculum terminale. Three-dimensional CT angiography revealed that the right VA was duplicated after emerging from the C-2 transverse foramen. One half of the duplication, an artery that was as large as the left VA, turned posteromedially and entered the spinal canal between C-1 and C-2. The other half, a very small artery, ran as usual and passed through the C-1 transverse foramen. The authors performed an occipitocervical posterior fusion and a C-1 laminectomy. Intraoperatively the course of the anomalous VA was identified on Doppler ultrasonography, and the surgical approach and bone excision were undertaken carefully to avoid VA injury. Postoperatively, resolution of myelopathy was marked. In the surgical treatment of patients with Down syndrome, surgeons should consider the possibility that a VA anomaly is present at the CVJ. With preoperative 3D CT angiography, the anomalous VA can be identified precisely and the possible risk of intraoperative VA injury predetermined.