This thesis is focused on the development of a user subroutine aimed to simulate the bone regeneration process through the finite element method. This research is important for enhancing surgical planning, implant design, and rehabilitation strategies for patients. Based on the mechanoregulation theory, tissue differentiation from granulation tissue to either fibrous, cartilage, or bone is governed by two mechanical factors: deviatoric strain and fluid flow. In this research, the theory was implemented through a custom user-subroutine for three cases: fractured tibia, the effects of implant stiffness and geometry evaluation, and mandibular reconstruction with particulate cancellous bone marrow (PCBM) grafts healing. In the fractured tibia cases, the developed user subroutine produced results that were consistent between the two-dimensional axisymmetric, solid 3D, and the reference models in terms of element distribution, tissue morphology, and interfragmentary strain. When evaluating the effects of implant stiffness and geometry, it was found that both of these factors play a crucial role in governing bone regeneration. The perfectly fitted implant generated a more rigid structure and a faster rate of bone regeneration compared to the implant with a 1 mm gap at the same Young’s modulus value. It was also demonstrated in this case that overly rigid implants can lead to significant bone resorption. Furthermore, the applicability of this theory to mandibular reconstruction with PCBM healing has been validated, as the simulation results showed good agreement with experimental findings in terms of tissue morphology, bone propagation patterns, and bone tissue fraction. Among the four simulated loading cases, the one with a 35% maximum bite force showed the best alignment with experimental data. It was observed that bone tissue propagates from the superior side and the buccal and lingual sides in contact with the native bone, starting from the outer regions and progressing inward. Additionally, diminishing trends in the maximum von Mises stress within the implants were observed as bone regeneration progressed.