The tendency to use a probabilistic design method rather than a deterministic design method for the design of nuclear power plants (NPPs) will increase because their safety should be considered and strictly controlled in relation to various causes of damage. The distance between a seismically isolated NPP structure and a moat wall is called the clearance to stop. The clearance to stop is obtained from the 90th percentile displacement response of a seismically isolated NPP subject to a beyond design basis earthquake (BDBE) in the probabilistic design method. The purpose of this study is to analyze the effects of heating and buckling effects on the 90th percentile displacement response of a lead-rubber bearing (LRB) subject to a BDBE. The analysis results show that considering the heating and buckling effects to estimate the clearance to stop is conservative in the evaluation of the 90th percentile displacement response. If these two effects are not taken into account in the calculation of the clearance to stop, the underestimation of the clearance to stop causes unexpected damage because of an increase in the collision probability between the moat wall and the seismically isolated NPP.