There are no reports comparing fluoroscopy and intraoperative computed tomography (CT) navigation in lateral single-position surgery (SPS) in terms of surgical outcomes or implant-related complications. Therefore, the purpose of this study was to use radiological evaluation to compare the incidence of instrument-related complications in SPS of lateral lumbar interbody fusion (LLIF) using fluoroscopy with that using CT navigation techniques. We evaluated 99 patients who underwent lateral SPS. Twenty-six patients had a percutaneous pedicle screw (PPS) inserted under fluoroscopy (SPS-C group), and 73 patients had a PPS inserted under intraoperative CT navigation (SPS-O group). Average operation time was shorter in the SPS-C group than in the SPS-O group (88.4 ± 24.4 min versus 111.9 ± 35.3 min, respectively, P = 0.003). However, there was no significant difference between the two groups in postoperative thigh symptoms or reoperation rate. The screw insertion angle of the SPS-C group was smaller than that of the SPS-O group, but there was no significant difference in the rate of screw misplacement (4.6% versus 3.4%, respectively, P = 0.556). By contrast, facet joint violation (FJV) was significantly lower in the SPS-O group than in the SPS-C group (8.4% versus 21.3%, respectively, P < 0.001). While fluoroscopy was superior to intraoperative CT navigation in terms of mean surgery time, there was no significant difference in the accuracy of PPS insertion between fluoroscopy and intraoperative CT navigation. The advantage of intraoperative CT navigation over fluoroscopy is that it significantly decreases the occurrence of FJV in SPS.