The reconstruction of craniomaxillofacial deformities, especially zygomatic bone repair, can be exigent due to the complex anatomical structure and the sensitivity of the crucial organs involved. The need to reconstruct the zygomatic bone in the most precise way is of crucial importance for enhancing the patient outcomes and health care-related quality of life (HRQL). Autogenous bone grafts, despite being the gold standard, do not match bone forms, have limited donor sites and bone volume, and can induce substantial surgical site morbidity, which may lead to adverse outcomes. The goal of this study is to provide an integrated approach that includes various processes, from patient scanning to implant manufacture, for the restoration of zygomatic bone abnormalities utilizing Polyetheretherketone (PEEK) material, while retaining adequate aesthetic and facial symmetry. This study takes an integrated approach, including computer-aided implant design using the mirror reconstruction technique, investigating the biomechanical behavior of the implant under loading conditions, and carrying out a fitting accuracy analysis of the PEEK implant fabricated using state-of-the-art additive manufacturing technology. The findings of the biomechanical analysis results reveal the largest stress of approximately 0.89 MPa, which is relatively low in contrast to the material’s yield strength and tensile strength. A high degree of sturdiness in the implant design is provided by the maximum value of strain and deformation, which is also relatively low at roughly 2.2 × 10−4 and 14 µm. This emphasizes the implant’s capability for load resistance and safety under heavy loading. The 3D-printed PEEK implant observed a maximum deviation of 0.4810 mm in the outside direction, suggesting that the aesthetic result or the fitting precision is adequate. The 3D-printed PEEK implant has the potential to supplant the zygoma bone in cases of severe zygomatic reconstructive deformities, while improving the fit, stability, and strength of the implant.