Basilar invagination (BI) is a rare anomaly of the craniovertebral junction. This report describes a rare case of BI with atlas assimilation and C1–2 joint ankylosis treated via a freehand condyle screw technique. A 71-year-old woman with progressive gait disturbance underwent a posterior-only procedure involving the release of the ankylosed C1–2 joint followed by distraction. Cranial fixation was achieved using bilateral condyle and C2 pedicle screws via a freehand technique under continuous intraoperative motor evoked potential (MEP) monitoring. Intraoperative MEPs significantly deteriorated following joint release and rod compression. Intraoperative X-rays revealed that specific head positions and segmental alignment changes were directly responsible for these MEP alterations. Prompt correction of the head position resulted in immediate MEP recovery. Postoperative computed tomography confirmed accurate screw placement, and the patient showed a normal neurological examination with no instability at the 1-year follow-up. Freehand condyle and C2 pedicle screw fixation is a viable and effective alternative to occipital plates for BI with atlas assimilation. Importantly, intraoperative MEP deterioration can be directly linked to changes in head position and segmental alignment. Prompt recognition and correction of these biomechanical changes are crucial for preventing neurological deficits during complex craniovertebral junction surgery.