This paper describes a fundamental study on the seismic safety margin for isolated structures using laminated rubber bearings. The variation of the seismic response assumed in the isolated structures will occur under the superposition of "Variations in seismic response due to input ground motions" and " Manufacturing error of the isolation devices". The seismic response analysis that allows for their conditions is important to assess the seismic safety margin for the isolated structures. The variation of the seismic response due to the superposition of these conditions can underestimate the seismic safety margin of the isolated structures. This paper clarifies that the seismic safety margin of the isolated structure, which consists of rubber bearings and oil dampers, for Sodium-cooled Fast Reactor (SFR) is ensured against the basis ground motions of the Japan Electric Association Guide 4601 (JEAG4601) and the SFR through the seismic response analyses. The seismic response analyses were performed by considering the superposition of the variation factors, such as the input ground motions and the manufacturing error of the isolation devices. Additionally, a relationship between the seismic safety margin and the excess probability of linearity limits was discussed using the results obtained from the seismic response analysis. The required seismic safety margins to satisfy the excess probability of linearity limits were clarified by that relationship.