Purpose: The aim of the present study was to compare the biomechanical effects of different lengths of implants in an immediate loading condition in mandibular and fibular bone. Three-dimensional (3D) nonlinear finite element analysis (FEA) was used to examine the complex irregular structures. The variables of this research were the two different bone types (mandible and fibula) and three different implant lengths. Materials and Methods: Simplified half models were constructed for 3D FEA. Three different implant lengths (6 mm, 10 mm, and 15 mm) were inserted into the mandibular and fibular bone models, which were made to simulate immediate implant loading conditions. A load of 125 N was applied to the center of the suprastructure at a 45-degree angle relative to the long axis of the implant, and the resultant maximum von Mises equivalent (EQV) stresses, stress distribution, strain energy, and micromotion were measured. Results: In the mandible, the maximum EQV stresses were 115.636 MPa, 155.943 MPa, and 157.105 MPa with the 6-mm, 10-mm, and 15-mm implants, respectively. The mean EQV stresses were 64.145 MPa, 77.925 MPa, and 78.500 MPa, respectively. In the fibula, the maximum EQV stresses were 174.04 MPa, 157.456 MPa, and 144.353 MPa with the 6-mm, 10-mm, and 15-mm implants, respectively. The mean EQV stresses were 82.329 MPa, 73.526 MPa, and 74.050 MPa, respectively. Conclusion: The micromotion in the fibula models was lower than that seen in the mandible models. EQV stress in the fibular bone was different from that in the mandible. Short implants can be an option for oral rehabilitation in the mandible; however, implants in the fibula should probably have bicortical engagement.