Background: Virtual surgical planning (VSP), via commercial services or developed in-house, has been applied to facilitate head and neck reconstruction. We evaluate a custom, automated planning software. Methods: Prospectively, VSP of 25 consecutive patients undergoing segmental mandibular reconstruction was performed. Postoperative CT was used to assess structural accuracy of VSP. Operative time, length of stay, and complication rate of the prospective cohort were compared with those of 25 consecutive retrospective historical cases. Results: The deviations between the plan and execution in mandibular width, projection, and volumetric overlap were 2.32 ± 3.91, 2.39 ± 1.72, and 0.59 ± 0.51 mm respectively. Compared with historical data, there was a significant reduction in operative time and length of stay, and no significant difference in complication rates. Conclusion: This is the largest prospective series evaluating an in-house VSP workflow for mandibular reconstruction and the first clinical evaluation of an automated planning platform.