Purpose Minimally invasive surgical techniques are advancing in spinal surgery, creating a need for the development of surgical support systems. This study evaluates the efficacy of a compact navigation system with smart delivery tools in percutaneous pedicle screw insertion. Methods This retrospective observational study included consecutive thoracic or lumbar spinal fusion patients with percutaneous pedicle screw placement treated from November 2022 to July 2023 in a Japanese private hospital. Primary outcomes were screw deviations (classified as any deviation, deviations of more than 2 mm, deviations from the medial to the caudal side). Pedicle screws were divided into two groups: those placed with the navigation system and those placed with traditional fluoroscopic guidance (non-navigation). Fisher's exact test and a generalized estimation equation for the prevalence ratio were conducted, adjusting for potential confounders. Results This study evaluated 492 pedicle screws (190 in the navigation group) in 78 patients. The median age was 70.5 years, and the most common condition was foraminal stenosis (26 patients, 33%). Of the study participants, 40 (51%) were male. Any deviation, deviations of more than 2 mm, and deviations from the medial to the caudal side were observed in 16 screws (8.4%) vs. 54 screws (21%) (p<
0.001), six screws (3.2%) vs. 31 screws (12%) (p<
0.001), and five screws (2.6%) vs. 10 screws (3.8%) (p=0.5) in the navigation and non-navigation groups, respectively. The adjusted prevalence ratios of the navigation group for any deviation, deviations of more than 2 mm, and deviations from the medial to the caudal side were 0.51 (95%CI 0.27, 0.98), 0.33 (95%CI 0.14, 0.78), and 0.88 (95%CI 0.26, 3.05), respectively. Conclusion This study suggests that compact navigation systems with smart delivery tools may improve screw placement accuracy in spinal surgeries.