A challenge of C2 pedicle screw placement is to avoid penetration into the C1-C2 facet joint, as this may alter normal biomechanics and accelerate joint degeneration. Our objective was to clarify how local anatomy and surgical technique may relate to C2 pedicle screw penetration into the C1-C2 facet joint. C2 pedicle screws were inserted using a fluoroscopically assisted freehand technique. Independent fellowship-trained spine surgeons blindly reviewed intraoperative fluoroscopic and postoperative computed tomography (CT) images for evidence of facet joint penetration (FJP). C2 pedicle morphometry, the sagittal angle of the facet joint, axial and sagittal pedicle screw angles, and screw length were measured on the relevant CT images. A total of 34 patients fulfilled the study criteria, and a total of 68 C2 pedicle screws were placed. Eight screws (16%) penetrated the C1-C2 facet joint. The mean sagittal angle of the C1-C2 facet joint was significantly lower in the FJP group compared with the non-FJP group. The mean sagittal angle of the screws was significantly higher in the FJP group compared with the non-FJP group. The mean screw length was significantly greater for screws causing FJP compared with the non-FJP group. The mean axial screw angle was significantly lower in the FJP group compared with the non-FJP group. Pedicle width, length, height, and transverse angle were not significantly associated with FJP. Independent reviewers were able to identify FJP on intraoperative fluoroscopic imaging in 2 out of 8 cases. Lower sagittal angle of the facet joint, higher sagittal angle of the pedicle screw, and screw length >24 mm are associated with higher risk of C1-C2 FJP. When placing C2 pedicle screws under these conditions, caution should be taken to avoid FJP. Several anatomical and technical factors may increase the risk of C1-C2 FJP during placement of C2 pedicle screws using a fluoroscopically assisted freehand technique, underscoring the importance of preoperative planning and limiting screw length.