In the design of breakwaters, the wave pressures out of the surf zone are estimated by the maximum wave height which corresponds to the 1.8 times of significant wave height according to Rayleigh theory. On the other hand, the nonlinear four-wave interactions can lead to a significant enhancement of occurrence frequency of extreme waves whose height can exceed above maximum wave height. It is necessary to appropriately evaluate the effects of the deviation from Rayleigh theory on the wave pressures acting on breakwaters under extreme wave conditions. In this study, the analyses of data obtained from the physical experiments in a wave tank were conducted through the comparison with the numerical simulations based on the Boussinesq equations. As a result, it is possible to evaluate the uncertainty of the wave pressures including the deviation from the Rayleigh theory by using the occurrence frequency of the maximum wave height depending on the kurtosis changing.