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Floods are natural disasters with significant socio-economic consequences. Urban areas with uncontrolled urban development, rapid population growth, an unregulated municipal system and an unplanned change of land use belong to the highly sensitive areas where floods cause devastating economic and social losses. The aim of this paper is to present a reliable GIS multi-criteria methodology for hazard zones’ mapping of flood-prone areas in urban areas. The proposed methodology is based on the combined application of geographical information systems (GIS) and multi-criteria decision analysis (MCDA). The methodology considers six factors that are relevant to the hazard of flooding in urban areas: the height, slope, distance to the sewage network, the distance from the water surface, the water table and land use. The expert evaluation takes into account the nature and severity of observed criteria, and it is tested using three scenarios: the modalities of the analytic hierarchy process (AHP). The first of them uses a new approach to the exploitation of uncertainty in the application of the AHP technique, the interval rough numbers (IR’AHP). The second one uses the fuzzy technique for the exploitation of uncertainty with the AHP method (F’AHP), and the third scenario contemplates the use of the traditional (crisp) AHP method. The proposed methodology is demonstrated in Palilula Municipality, Belgrade, Serbia. In the last few decades, Palilula Municipality has been repeatedly devastated by extreme flood events. These floods severely affected the transportation networks and other infrastructure. Historical flood inundation data have been used in the validation process. The final urban flood hazard map proves a satisfactory agreement between the flood hazard zones and the spatial distribution of historical floods that happened in the last 58 years. The results indicate that the scenario in which the IR’AHP methodology is used provides the highest level of compatibility with historical data on floods. The produced map showed that the areas of very high flood hazard are located on the left Danube River bank. These areas are characterized by lowland morphology, gentle slope, sewage network, expansion of impermeable locations and intense urbanization. The proposed GIS-IR’AHP methodology and the results of this study provide a good basis for developing a system of flood hazard management in urban areas and can be successfully used for spatial city development policy.