Methods: Clinical and radiological features of 18 patients with CV junction abnormalities were analyzed between March 2017 and February 2019 at Sawai Man Singh Medical College, Jaipur, India. Dynamic computed tomography (CT) of the CV junction and CT angiographies of the neck with respect to the vertebral artery course at the C1–C2 joints were obtained and studied. Customized 3D models of the CV junction were then made based on the CT data, and rehearsal of the surgical procedure was performed using the 3D model one day prior to performing the actual procedure. Results: Seventeen patients had congenital-type AAD, whereas one patient had posttraumatic AAD. Improvements in neck pain and myelopathy were seen in all patients at the follow-up, as analyzed using the Visual Analog Scale and the Japanese Orthopedic Association Scale score, respectively. There were no cases of malpositioning of screws or any direct vertebral artery injury, although in one patient, the distal flow in the dominant vertebral artery was cut off as it got compressed between the bony arch and the screw head. Conclusions Compared to computer-generated images, 3D-printed models are a more practical approach for dealing with complex CV junction abnormalities. They provide surgeons with deep insights into the complex bony anomalies as well as variations in the vertebral artery courses, thereby improving surgical outcomes.