In the seismic safety assessment and design of building structures in nuclear facilities, lumped mass models are conventionally used. However, they cannot possess the required high-accuracy evaluation of nuclear facilities, such as the local response at the equipment location in a reactor building. From this point of view, a seismic response analysis method using a three-dimensional finite element (3D FE) model is indispensable. Furthermore, because analysis results obtained using 3D FE models vary to a large degree depending on the experience and knowledge of analysts, the quality of analysis results should be ensured by developing a standard analysis method. In the Japan Atomic Energy Agency, we have developed a guideline for seismic response analysis methods that adopt 3D FE models of reactor buildings, and we plan to publish it as JAEA report. The guideline consists of a main body, commentary, and several appendixes; it also includes procedures, recommendations, points of attention, and a technical basis for conducting seismic response analysis using 3D FE models of reactor buildings. In this paper, the outline of the guideline and analysis examples based on the guideline are presented.