This study intends to evaluate the conservativeness of the fixed-base analysis as compared to the soil-structure interaction (SSI) analysis for the seismically isolated model of a nuclear power plant in Korea. To that goal, the boundary reaction method (BRM), combining frequency-domain and time-domain analyses in a twofold process, is adopted for the SSI analysis considering the nonlinearity of the seismic base isolation. The program KIESSI-3D is used for computing the reaction forces in the frequency domain and the program MIDAS/Civil is applied for the nonlinear time-domain analysis. The BRM numerical model is verified by comparing the results of the frequency-domain analysis and time-domain analysis for the soil-structure system with an equivalent linear base isolation model. Moreover, the displacement response of the base isolation and the horizontal response at the top of the structure obtained by the nonlinear SSI analysis using BRM are compared with those obtained by the fixed-base analysis. The comparison reveals that the fixed-base analysis provides conservative peak deformation for the base isolation but is not particularly conservative in term of the floor response spectrum of the superstructure.