During a scenario earthquake with M_W9.0 along the Nankai Trough, strong ground motion is expected in the focal area, Wakayama Prefecture, Japan. In order to simulate the seismic damage of railway structures, it is necessary to estimate strong motions at the sites of interest with sufficient accuracy, taking into account local site effects. In this study, seismic waveforms at 54 sites for permanent railway station along JR Kinokuni Line were predicted based on the SMGA models considering the empirical site amplification and phase effects. The predicted seismic waveforms will be useful for rational safety assessment of a railway structure.