BACKGROUND CONTEXT: Studies have shown biomechanical superiority of cervical pedicle screw placement over other techniques. However, accurate placement is challenging due to the inherent risk of neurovascular complications. Navigation technology based on intraoperative 3D imaging allows highly accurate screw placement, yet studies specifically investigating screw placement in patients with traumatic atlantoaxial injuries are scarce. The aim of this study was to compare atlantoaxial screw placement as treatment of traumatic instabilities using iCT-based navigation or fluoroscopic-guidance with intraoperative 3D control scans. METHODS: This was a retrospective review of patients with traumatic atlantoaxial injuries treated operatively with dorsal stabilization of C1 and C2. Patients were either assigned to the intraoperative navigation or fluoroscopic-guidance group. Screw accuracy, procedure time, and revisions were compared. RESULTS: Seventy-eight patients were included in this study with 51 patients in the navigation group and 27 patients in the fluoroscopic-guidance group. In total, 312 screws were placed in C1 and C2. Screw accuracy was high in both groups; however, pedicle perforations > 1 mm occurred significantly more often in the fluoroscopic-guidance group (P = 0.02). Procedure time was on average 23 min shorter in the navigation group (P = 0.02). CONCLUSIONS: This study contributes to the available data showing that navigated atlantoaxial screw placement proves to be feasible as well as highly accurate compared to the fluoroscopic-guidance technique without prolonging the time needed for surgery. When comparing these data with other studies, the application of different classification systems for assessment of screw accuracy should be considered.