Although Egypt may be considered as an area of low seismicity, it has experienced the recurring destructive effects of earthquakes throughout its history. The damage distribution is significantly affected by fault geometry and the local site effects. Thus, an appropriate assessment of seismic hazard became a major challenge for efficient mitigation of the seismic risk. This study develops the Geographical Information System (GIS) based three-dimensional (3D) deterministic model to evaluate the seismic hazard map for specified seismic source fault for Egypt. The geometry of a fault plane is generated by a fault-modeling algorithm in which multiple 3D plane sets are interpreted by fault trace, geology, and topography. For estimating the local site effects, the study area is modeled by a 3D grid-mesh system and the ground motion propagation is estimated at each grid by considering the spatial analysis of average shear-wave velocity and a soil susceptibility map. The developed model is applied to simulate the seismic hazard maps in particular the October 12, 1992, Dahshour earthquake that caused huge disasters. The simulated seismic hazard maps of the October 12, 1992, Dahshour earthquake are validated at the observation of an isoseismal map and the evidence of the locations that caused serious damages. Furthermore, an evaluation of the expected Dahshour earthquake with magnitude 6.5 and October 11, 1999, Beni Suef earthquake is conducted for seismic risk mitigation study. By utilizing the developed model, our results encourage the GIS approach for seismic hazard analysis where 3D models can lead to a more accurate assessment.