Percutaneous pedicle screws (PPSs) are commonly used in posterior spinal fusion to treat spine conditions such as trauma, tumors, and degenerative diseases. Precise PPS placement is essential in preventing neurological complications and improving patient outcomes. Recent studies have suggested that intraoperative computed tomography (CT) navigation can reduce the dependence on extensive surgical expertise for achieving accurate PPS placement. However, more comprehensive documentation is needed regarding the procedural accuracy of lateral spine surgery (LSS). In this retrospective study, we investigated patients who underwent posterior instrumentation with PPSs in the thoracic to lumbar spine, utilizing an intraoperative CT navigation system, between April 2019 and September 2023. The system’s methodology involved real-time CT-based guidance during PPS placement, ensuring precision. Our study included 170 patients (151 undergoing LLIF procedures and 19 trauma patients), resulting in 836 PPS placements. The overall PPS deviation rate, assessed using the Ravi scale, was 2.5%, with a notably higher incidence of deviations observed in the thoracic spine (7.4%) compared to the lumbar spine (1.9%). Interestingly, we found no statistically significant difference in screw deviation rates between upside and downside PPS placements. Regarding perioperative complications, three patients experienced issues related to intraoperative CT navigation. The observed higher rate of inaccuracies in the thoracic spine suggests that various factors may contribute to these differences in accuracy, including screw size and anatomical variations. Further research is required to refine PPS insertion techniques, particularly in the context of LSS. In conclusion, this retrospective study sheds light on the challenges associated with achieving precise PPS placement in the lateral decubitus position, with a significantly higher deviation rate observed in the thoracic spine compared to the lumbar spine. This study emphasizes the need for ongoing research to improve PPS insertion techniques, leading to enhanced patient outcomes in spine surgery.