This article presents a nonlinear site amplification model for ground‐motion prediction equations (GMPEs), using site period as site‐effect proxy based on the measured shear‐wave velocity profiles of selected KiK‐net and K‐NET sites in Japan. This model was derived using 1D equivalent‐linear site‐response analysis for a total of 516 measured soil‐site shear‐wave velocity profiles subjected to a total of 912 components of rock‐site records. The modulus reduction and damping curves for each soil layer were assigned based on the soil‐type description for a particular layer. The site period and site impedance ratio affect both the linear and nonlinear parts of this study, and were used as the site parameters in the 1D amplification model. A large impedance ratio enhances the amplification ratios when the site responds elastically and enhances the nonlinear response when the site develops a significant nonlinear response. The effects of moment magnitude and source distance on the linear part of the 1D amplification model were also incorporated in the model. To implement the 1D amplification model into GMPEs, a model adjustment is required to match the GMPE amplification ratio at weak motion and to retain the nonlinear amplification ratio at the strong motion of the 1D model. The two‐step adjustment method by Zhao, Hu, et al. (2015) was adopted in this study with significant modifications. It is not possible to obtain a credible second‐step adjustment parameter using the GMPEs dataset only. We proposed three methods for calculating the scale factors. Method 1 is a constant angle in a 30°–60° range for all spectral periods; method 2 was based on the GMPE dataset and 1‐D model parameters; and method 3 was based on the strong‐motion records used for the 1D site modeling. A simple second‐step adjustment factor leads to smoothing amplification ratios and soil‐site spectrum.