Spatial variations of a seismic wave are mainly wave passage and wave scattering. Wave passage effect is produced by changed characteristics of exciting seismic input motions applied to the bedrock. Modified input motions travel horizontally with time differences determined by apparent shear wave velocity of the bedrock. In this study, wave passage effect on the seismic response of a structure-soil system is investigated by modifying the finite element software of P3DASS (Pseudo 3-Dimensional Dynamic Analysis of a Structure-soil System) to apply inconsistent (time-delayed) seismic input motions along the soft soil–bedrock interface. Study results show that foundation size affected on the seismic response of a structure excited with inconsistent input motions in the lower period range below 0.5 seconds, and seismic responses of a structure were decreased considerably in the lower period range around 0.05 seconds due to the wave passage. Also, shear wave velocity of the bedrock affected on the seismic response of a structure in the lower period range below 0.3 seconds, with significant reduction of the seismic response for smaller shear wave velocity of the bedrock reaching approximately 20% for an apparent shear wave velocity of 1000m/s at a period of 0.05 seconds. Finally, it is concluded that wave passage effect reduces the seismic response of a structure in the lower period range when the bedrock under a soft soil is soft or the bedrock is located very deeply, and wave passage is beneficial for the seismic design of a short period structure like a nuclear container building or a stiff low-rise building.