Atlantoaxial instability (AAI)/subluxation commonly occurs in small breed dogs. Ventral stabilization techniques using screws and/or pins and a plate or, more commonly, polymethylmethacrylate are considered to provide the most favorable outcome. However, the implantation of screws of sufficient sizes for long-term stability becomes challenging in toy breed dogs (e.g. <2 kg). We herein report the application of 3D printing technology to implant trajectory planning and implant designing for the surgical management of AAI in 18 dogs. The use of our patient-specific drill guide templates resulted in overall mean screw corridor deviations of less than 1 mm in the atlas and axis, which contributed to avoiding iatrogenic injury to the surrounding structures. The patient-specific titanium plate was effective for stabilizing the AA joint and provided clinical benefits to 83.3% of cases (15/18). Implant failure requiring revision surgery occurred in only one case, and the cause appeared to be related to the suboptimal screw-plate interface. Although further modifications are needed, our study demonstrated the potential of 3D printing technology to be effectively applied to spinal stabilization surgeries for small breed dogs, allowing for the accurate placement of screws and minimizing peri- and postoperative complications, particularly at anatomical locations at which screw corridors are narrow and technically demanding.