For preoperative evaluation of the vertebral artery (VA) at the craniovertebral junction, 3-dimensional (3-D) computed tomography (CT) angiography can simultaneously and precisely depict the location of the VA and the circumferential osseous tissues. However, this procedure has the risk of contrast-induced nephropathy, especially when patients have pre-existing renal impairment. We report the case of a 73-year-old woman with rheumatoid arthritis and concomitant chronic renal failure in whom severe myelopathy developed due to atlantoaxial vertical subluxation and subaxial subluxation. We planned to perform C1 laminectomy and C3-C7 laminoplasty, but to avoid the risk of intraoperative VA injury, we applied a fusion image technique of 3-D magnetic resonance (MR) angiography and co-registered 3-D CT that allowed for virtual assessment preoperatively of the VA courses, instead of 3-D CT angiography. Through the 3-D hybrid MR angiography-CT images, we could predict, in detail, the VA courses and the surrounding bony structures. At surgery, we found that the locations of the VAs were identical to that predicted on the preoperative image fusion analysis. We conclude that our image fusion techniques possess accurate diagnostic value for detecting arterial course, and could be applicable for patients in whom administration of contrast media should be avoided due to specific conditions, such as drug allergy and chronic renal failure.