This study aims to evaluate the safety and efficacy of the ultrasonic bone burr (UBB) in facilitating C1 pedicle screw placement for atlantoaxial instability (AAI) treatment, compared to the conventional high-speed drill (HSD) technique. A retrospective analysis was conducted on patients undergoing posterior screw-rod fixation for AAI between December 2017 and July 2023. The patients were divided into two groups based on the tools used for screw placement: UBB and HSD. Data on surgical duration, estimated blood loss, spinal cord and arterial injury incidence, screw placement accuracy, neurological status measured by the Japanese Orthopedic Association (JOA) score and fusion rates, were collected and analyzed. 13 patients received C1 pedicle screw placement via UBB facilitation, while 8 were treated using the HSD approach. The UBB group showed a significant reduction in blood loss and operation time compared to the HSD group (P=0.002 and P<0.001, respectively). No spinal cord or arterial injuries occurred in either group. Optimal screw placement was confirmed in all UBB cases versus 87.5% in the HSD group (P=0.139). Both groups demonstrated significant improvements in JOA scores with no inter-group difference. The fusion rate was 100% in the UBB group and 87.5% in the HSD group, not statistically different (P=0.381). UBB is a viable alternative for C1 pedicle screw placement, associated with reduced blood loss and shorter operation time, while achieving comparable clinical outcomes to the conventional HSD method. Nevertheless, further research with a larger sample size is needed.