Cervical pedicle screw (CPS) fixation provides high stability but poses a risk of nerve and vascular injury. Although useful for reducing CPS deviation rates, navigation systems cannot completely eliminate deviation. This study aimed to compare two methods for creating insertion paths, one using a navigation-linked high-speed drill (NAVI drill) and the other using conventional manual probing. Our study comprised 104 patients with 509 CPSs at the C3-6 level who were treated at our institution between 2017 and 2023. CPS deviations were graded according to the Neo classification system, and the deviation direction (medial, lateral, cranial, or caudal) was assessed. Complications associated with CPS deviation were also investigated. We compared cases that used the NAVI drill (Group M) with those that used manual probing (Group N). Group M included 45 cases (252 screws), and Group N included 59 cases (257 screws). The CPS deviation rate was grade 1 or higher in 14.7% and 17.1% of cases in Groups M and N, respectively (p = 0.469). It was grade 2 or higher in 1.2% and 4.3% of cases in Groups M and N, respectively (p = 0.222). The medial, lateral, caudal, and cranial deviation direction rates were 56.8%, 2.7%, 40.5%, and 0% in Group M and 13.6%, 72.7%, 11.4%, and2.3% in Group N, respectively (p < 0.001). In one case in Group N, a grade 3 lateral deviation resulted in vertebral artery injury (VAI). The use of the NAVI drill was associated with a slightly lower, albeit insignificant, CPS deviation rate. However, it significantly lowered the proportion of lateral deviations. Therefore, the NAVI drill is a useful tool for preventing VAI.