To assess the accuracy of O-arm-navigation-based pedicle screw insertion in dystrophic scoliosis secondary to NF-1 and compare it with free-hand pedicle screw insertion technique. 32 patients with dystrophic NF-1-associated scoliosis were divided into two groups. A total of 92 pedicle screws were implanted in apical region (two vertebrae above and below the apex each) in 13 patients using O-arm-based navigation (O-arm group), and 121 screws were implanted in 19 patients using free-hand technique (free-hand group). The postoperative CT images were reviewed and analyzed for pedicle violation. The screw penetration was divided into four grades: grade 0 (ideal placement), grade 1 (penetration <2mm), grade 2 (penetration between 2 and 4mm), and grade 3 (penetration >4mm). The accuracy rate of pedicle screw placement (grade 0, 1) was significantly higher in the O-arm group (79%, 73/92) compared to 67% (81/121) of the free-hand group (P=0.045). Meanwhile, a significantly lower prevalence of grade 2-3 perforation was observed in the O-arm group (21 vs. 33%, P<0.05), and the incidence of medial perforation was significantly minimized by using O-arm navigation compared to free-hand technique (2 vs. 15%, P<0.01). Moreover, the implant density in apical region was significantly elevated by using O-arm navigation (58 vs. 42%, P<0.001). We reported 79% accuracy of O-arm-based pedicle screw placement in dystrophic NF-1-associated scoliosis. O-arm navigation system does facilitate pedicle screw insertion in dystrophic NF-1-associated scoliosis, demonstrating superiorities in the safety and accuracy of pedicle screw placement in comparison with free-hand technique.