This paper presents a detailed procedure for a nonlinear soil-structure interaction of a seismically isolated NPP(Nuclear Power Plant) structure using the boundary reaction method (BRM). The BRM offers a two-step method as follows: (1) the calculation of boundary reaction forces in the frequency domain on an interface of linear and nonlinear regions, (2) solving the wave radiation problem subjected to the boundary reaction forces in the time domain. For the purpose of calculating the boundary reaction forces at the base of the isolator, the KIESSI-3D program is employed in this study to solve soil-foundation interaction problem subjected to vertically incident seismic waves. Wave radiation analysis is also employed, in which the nonlinear structure and the linear soil region are modeled by finite elements and energy absorbing elements on the outer model boundary using a general purpose nonlinear FE program. In this study, the MIDAS/Civil program is employed for modeling the wave radiation problem. In order to absorb the outgoing elastic waves to the unbounded soil region, spring and viscous-damper elements are used at the outer FE boundary. The BRM technique utilizing KIESSI-3D and MIDAS/Civil programs is verified using a linear soil-structure analysis problem. Finally the method is applied to nonlinear seismic analysis of a base-isolated NPP structure. The results show that BRM can effectively be applied to nonlinear soil-structure interaction problems.