End-stage temporomandibular joint (TMJ) disorders often necessitate total joint replacement, and the selection of biomaterial directly impacts long-term outcomes. Ti6Al4V and CoCrMo are commonly used alloys, yet their biomechanical performance in patient-specific prostheses remains insufficiently compared. This study aimed to evaluate the mechanical response of custom TMJ prostheses fabricated from these alloys using finite element analysis (FEA). A three-dimensional mandibular model was created from computed tomography data, and a patient-specific prosthesis was designed in SolidWorks (Dassault Systèmes, SolidWorks Corp., Waltham, MA, USA) and analyzed in ANSYS Workbench 2022 R1 (Ansys Inc., Canonsburg, PA, USA). Physiological loading was simulated by applying forces at the insertion sites of the temporalis, masseter, and medial pterygoid muscles. In the Ti6Al4V model, maximum von Mises stresses reached 192.18 MPa on the mandibular component and 92.004 MPa on the fossa prosthesis, whereas the CoCrMo model demonstrated higher stresses of 204.31 MPa and 94.182 MPa, respectively. Both alloys exhibited similar stress distributions, but Ti6Al4V generated lower stress magnitudes, indicating more favorable load transfer and a reduced risk of mechanical overload on articulating components. These findings underscore the significance of alloy selection in optimizing TMJ prostheses and demonstrate the value of FEA as a tool for guiding future patient-specific designs.