Seismic analysis of small and medium nuclear reactor (SMR) plants is of utmost importance for their safe design and operation. Terrain effect, which is often neglected in traditional analysis approaches, is one of the important parameters for site-specific seismic characterization. A hybrid boundary/finite element method (BEM–FEM) is applied to account for the seismic response of nuclear power plants in a rugged terrain. A 3D hybrid BEM–FEM model of a pair of nuclear power plants located in the footstep of a mountainous region is developed. The boundary element method (BEM) is used to model the far-field irregular topography. Finite element method (FEM) is used to model the near-field soil, foundation, and the superstructure of the main and auxiliary buildings of the nuclear power plant. The analytical expression for time-harmonic free-field motion is used to simulate the incident seismic wavefield. The results include the seismic responses of the two nuclear power plant structures that account for the terrain effects.