Induced contraction of the suprahyoid muscles via magnetic stimulation is considered to be effective for the rehabilitation of dysphagia. In our previous study, a magnetic stimulation coil with a U-shaped core for stimulating the suprahyoid muscles was developed based on the results of numerical analysis using a simplified human head model. It was confirmed that magnetic stimulation by the coil causes large contraction of the muscles. However, the human head has a complex structure that includes bone structures through which current cannot easily pass. To accurately predict the current density distribution induced by magnetic stimulation, a model that accurately describes the human head is required for numerical analysis. Therefore, in this study, numerical analysis using the finite element method with a human head model that includes the bone structure obtained from computed tomography scans was performed. The results for the model with bone structure show that the coil with a U-shaped core can stimulate the motor points of the suprahyoid muscles in the middle of the submental region. When compared with the current density observed in a model without the bone structure, that in the model with the bone structure was reduced by 29% at a point 20 mm below the mandibular surface. It is thus necessary to perform a numerical analysis using a model with the bone structure to obtain accurate analysis results.