Most of earthquake-induced geotechnical hazards have been caused by the site effects relating to the amplification of ground motion, which is strongly influenced by the local geologic conditions such as soil thickness or bedrock depth and soil stiffness. In this study, an integrated GIS-based information system for geotechnical data, called geotechnical information system (GTIS), was constructed to establish a regional counterplan against earthquake-induced hazards at an urban area of Daejeon, which is represented as a hub of research and development in Korea. To build the GTIS for the area concerned, pre-existing geotechnical data collections were performed across the extended area including the study area and site visits were additionally carried out to acquire surface geo-knowledge data. For practical application of the GTIS used to estimate the site effects at the area concerned, seismic zoning map of the site period was created and presented as regional synthetic strategy for earthquake-induced hazards prediction. In addition, seismic zonation for site classification according to the spatial distribution of the site period was also performed to determine the site amplification coefficients for seismic design and seismic performance evaluation at any site in the study area. Based on this case study on seismic zonations in Daejeon, it was verified that the GIS-based GTIS was very useful for the regional prediction of seismic hazards and also the decision support for seismic hazard mitigation.