As a result of ongoing urbanization and climate change, urban areas (e.g., Gaza Strip (GS)) experienced many floods recently. These floods posed threats to human lives and turned many regions to disaster areas; however, municipalities’ managers attempt to combat this challenge. This study aims to present a geographic information system multi-criteria decision analysis (GIS-MCDA) method to identify flood-prone areas. Five criteria are considered: distance to stormwater drainage network, land use (cover), height, slope, and groundwater depth. Three steps are carried out to classify the areas according to its vulnerability to flooding into five categories: “Very high,” “High,” “Moderate,” “Low,” and “Very low.” These steps are the following: standardization, weighting, and overlaying of the criteria. After that, a sensitivity analysis was performed to show how areas’ classes are changed. The proposed methodology was demonstrated in Gaza Governorate (Palestine) were most people and infrastructures were severely affected by flood in the last two decades. The results show that Nafaq Street, Zaytoon, Toffah, and Daraj regions are the most vulnerable areas in Gaza Governorate. This was consistent with historical floods inundation data. This study is a powerful tool with low cost and time that guides decision-makers to allocate the proper management in flood-prone areas in Gaza Governorate. Further research includes taking advantage of the flood-prone area map to implement spreading managed aquifer recharge projects.