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Background: Excess flexion or extension during occipitocervical fusion (OCF) can lead to postoperative complications, such as dysphagia, respiratory problems, line of sight issues, and neck pain, but posterior fossa decompression (PFD) and OCF require different positions that require intraoperative manipulation. Objective: The objective of this study was to describe quantitative fluoroscopic morphometrics in Chiari malformation (CM) patients with symptoms of craniocervical instability (CCI) and demonstrate the intraoperative application of these measurements to achieve neutral craniocervical alignment while leveraging a single axis of motion with the Mayfield head clamp locking mechanism. Methods: A retrospective cohort study of patients with CM 1 and 1.5 and features of CCI who underwent PFD and OCF at a single-center institution from March 2015 to October 2020 was performed. Patient demographics, preoperative presentation, radiographic morphometrics, operative details, complications, and clinical outcomes were analyzed. Results: A total of 39 patients met the inclusion criteria, of which 37 patients (94.9%) did not require additional revision surgery after PFD and OCF. In this nonrevision cohort, preoperative to postoperative occipital to C2 angle (O-C2a) (13.5° ± 10.4° vs. 17.5° ± 10.1°, P = 0.047) and narrowest oropharyngeal airway space (nPAS) (10.9 ± 3.4 mm vs. 13.1 ± 4.8 mm, P = 0.007) increased significantly. These measurements were decreased in the two patients who required revision surgery due to postoperative dysphagia (mean difference - 16.6°° in O C2a and 12.8°° in occipital and external acoustic meatus to axis angle). Based on these results, these fluoroscopic morphometrics are intraoperatively assessed, utilizing a locking Mayfield head clamp repositioning maneuver to optimize craniocervical alignment prior to rod placement from the occipital plate to cervical screws. Conclusion: Establishing a preoperative baseline of reliable fluoroscopic morphometrics can guide surgeons intraoperatively in appropriate patient realignment during combined PFD and OCF, and may prevent postoperative complications.