The seismic isolation system makes a structure isolated from ground motions to protect the structure from seismic events. Seismic isolation techniques have been implemented in full-scale buildings and bridges because of their simplicity, economic effectiveness, inherent stability and reliability. As for the responses of an isolated structure due to seismic events, it is well known that the most uncertain aspects are the seismic loading itself and structural properties. Due to the randomness of earthquakes and uncertainty of structures, seismic response distributions of an isolated structure are needed when evaluating the seismic fragility assessment (or probabilistic seismic safety assessment) of an isolated structure. Seismic response time histories are useful and often essential elements in its design or evaluation stage. Thus, a large number of non-linear dynamic analyses should be performed to evaluate the seismic performance of an isolated structure. However, it is a monumental task to gather the design or evaluation information of the isolated structure from too many seismic analyses, which is impractical. In this paper, a new methodology that can evaluate the seismic fragility assessment of an isolated structure is proposed by using stochastic response database, which is a device that can estimate the seismic response distributions of an isolated structure without any seismic response analyses. The seismic fragility assessment of the isolated nuclear power plant is performed using the proposed methodology. The proposed methodology is able to evaluate the seismic performance of isolated structures effectively and reduce the computational efforts tremendously.