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Background The optimal treatment strategy for Pauwels type III femoral neck fractures remains controversial. A new internal fixation femoral neck system (FNS) for the treatment of femoral neck fractures was developed, and we compared the mechanical efficiency of the internal fixation FNS with that of two cannulated screw configurations for the treatment of Pauwels type III femoral neck fractures. Method: In this study, we constructed models of Pauwels type III femoral neck fractures with angles of 50°, 60°, and 70°. Moreover, a fixation model with the FNS and two fixation models with cannulated screws were developed. Under two axial loads, 1400 N and 2100 N, the von Mises stress distributions, maximum von Mises stress, and displacements of the femur and internal fixation components were measured for each fracture group. Result The maximum von Mises stress of internal fixation in the three models was mostly located near the fracture line, and the femoral head region closest to the femoral calcar experienced the maximum amount of stress. As the Pauwels angle and axial loads increased, the stress and displacement of the proximal femoral head and internal fixation component increased in each group. Compared with cannulated screw configurations, the internal fixation FNS showed lower values of peak stress at the femoral head and smaller displacements of the femur and internal implant in the treatment of Pauwels type III femoral neck fractures with Pauwels angles of 50°, 60°, and 70°. Conclusion The newly developed internal fixation FNS provided improved biomechanical stability for the treatment of Pauwels type III femoral neck fractures, which indicated that the internal fixation FNS may be a new option for the treatment of vertical femoral neck fractures.