The 2017 Pohang earthquake afflicted more significant economic losses than the 2016 Gyeongju earthquake, even if these earthquakes had a similar moment magnitude. This phenomenon could be due to local site conditions that amplify ground motions. Local site effects could be estimated from methods using the horizontal-to-vertical spectral ratio, standard spectral ratio, and the generalized inversion technique. Since the generalized inversion method could estimate the site effect effectively, this study modeled the site effects in the Korean peninsula using the generalized inversion technique and the Fourier amplitude spectrum of ground motions. To validate the method, the site effects estimated for seismic stations were tested using recorded ground motions, and a ground motion prediction equation was developed without considering site effects.