The purpose of the study was to compare the accuracy of computer-assisted surgery (CAS) and the traditional freehand technique for fibular free flap mandibular reconstruction as well as to evaluate the accuracy of the CAS planning. The medical records of 18 patients who underwent mandibular reconstruction with fibular free flap were reviewed. The CAS group (n = 7) benefited from virtual surgical planning and custom patient-specific plates and surgical cutting guides. The Control group (n = 11) was treated by conventional surgery. Morphometric comparison was done by calculating the differences in specific linear and angular parameters on pre- and postoperative CT-scans for both groups by using ProPlan CMF(®) software. Symmetry was also assessed by calculating the ratio of the affected versus the nonaffected side. In the CAS group, planned and postoperative CT-scans were compared to evaluate accuracy. The morphometric comparison showed no statistically significant differences between the groups except for the axial angle on the nonaffected side (mean difference 1.0° in the CAS group versus 2.9° in the Control group; p = 0.03). Ratios of the affected side over the nonaffected side showed no differences between the two groups. In the CAS group, the accuracy assessment showed a mean distance deviation of 2.3 mm for mandibular osteotomies and 1.9 mm for fibular osteotomies. Our results indicated that CAS and the conventional freehand techniques were comparable in their ability to provide a satisfactory morphological fibular free flap mandibular reconstruction. Moreover, the accuracy of the CAS technique was within the range reported in the literature.