Objective : To identify the accuracy and efficiency of the computed tomographic (CT)-based navigation system on upper cervical instrumentation, particularly C1 lateral mass and C2 pedicle screw fixation compared to previous reports. Methods : Between May 2005 and March 2014, 25 patients underwent upper cervical instrumentation via a CT-based navigation system. Seven patients were excluded, while 18 patients were involved. There were 13 males and five females; resulting in four degenerative cervical diseases and 14 trauma cases. A CT-based navigation system and lateral fluoroscopy were used during the screw instrumentation procedure. Among the 58 screws inserted as C1-2 screws fixation, their precise positions were evaluated by postoperative CT scans and classified into three categories : in-pedicle, non-critical breach, and critical breach. Results : Postoperatively, the precise positions of the C1-2 screws fixation were 81.1% (47/58), and 8.6% (5/58) were of non-critical breach, while 10.3% (6/58) were of critical breach. Most (5/6, 83.3%) of the critical breaches and all of non-critical breaches were observed in the C2 pedicle screws and there was only one case of a critical breach among the C1 lateral mass screws. There were three complications (two vertebral artery occlusions and a deep wound infection), but no postoperative instrument-related neurological deteriorations were seen, even in the critical breach cases. Conclusion : Although CT-based navigation systems can result in a more precise procedure, there are still some problems at the upper cervical spine levels, where the anatomy is highly variable. Even though there were no catastrophic complications, more experience are needed for safer procedure.