A parallel finite element method (FEM) based on high-fidelity models for solving diverse earthquake engineering problems is presented. Its key feature is a parallel solver that is tuned to solve large-scale wave equations. Tensorial material constitutive relations of concrete and soil and sophisticated nonlinear joint elements are implemented to broaden the applicability of the parallel FEM. The performance of the proposed parallel FEM is demonstrated for three examples; namely, seismic response, liquefaction, and surface earthquake fault analyses. A high-fidelity model was constructed for each analysis, and the numerical results were validated against observed data. The performance of the proposed parallel FEM approach was evaluated in terms of the resolution of the simulated results.Ensemble computing based on approximately a hundred high-fidelity models is useful for cases where there are considerable uncertainties regarding the material properties.