The finite element method is a practical tool to compute the response of the irregularly layered soil deposit to the base-rock motions. The method is useful not only in estimating the interaction between the structure and the surrounding soil as a whole and the local behavior of the contacting area in detail, but also in predicting the resulting behavior of the superstructure affected by such soil-structure interactions. However, the computation of finite element analysis is marched in the time domain (TD), while the site response analysis has been carried out mostly in the frequency domain (FD) with equivalent linear analysis. This study is intended to compare the results of the TD and FD analysis with focus on the peak response accelerations and the predominant frequencies, and thus to evaluate the applicability and the validity of the finite element analysis in the site response analysis. The comparison shows that one can obtain the results very close to that of FD analysis, from the finite element analysis by including sufficiently large width of foundation in the model and further by applying partial mode superposition. The finite element analysis turned out to be well agreeing with FD analysis in their computed results of the peak acceleration and the acceleration response spectra, especially at the surface layer.