Preoperative computed tomography (CT)-based navigation is used for cervical pedicle screw (CPS) insertion to mitigate the risk of spinal cord and vertebral artery injury. In vertebrae with osteosclerosis due to degeneration or other factors, however, probing may not proceed easily, with difficulty creating the CPS insertion hole. This study investigated the impact of osteosclerosis on the accuracy of CPS insertion. A total of 138 patients with CPS inserted at the C3-C7 level using preoperative CT navigation were retrospectively analyzed. Pre- and postoperative CT was employed to investigate screw position and Hounsfield unit (HU) values at the lateral mass to evaluate the degree of osteosclerosis in the CPS insertion pathway. Among 561 CPS insertions, the Grade 3 perforation rate was 1.8%, and the Grade 2 or higher perforation rate was 8.0%. When comparing insertions with and without CPS perforation, HU values were significantly higher in the perforation group (578 ± 191 vs. 318 ± 191, p < 0.01). The frequency of CPS insertion into the mid-cervical spine was also significantly greater in the perforation group (68.9% vs. 62.5%, p < 0.01). Logistic regression analysis revealed that a high HU value at the lateral mass (odds ratio 1.09, 95% confidence interval: 1.07-1.11, p < 0.01) was a significant independent factor associated with CPS deviation. The screw perforation rate of Grade 2 or higher in CPS insertion using preoperative CT-based navigation was 8.0%. Since osteosclerosis was an independent factor related to CPS deviation, additional care may be required during insertion into affected vertebrae.