In the current context of fast innovation in the field of urban resilience against extreme weather events, it is becoming more challenging for decision-makers to recognize the most beneficial adaptation measures for their cities. Detailed assessment of multiple measures is resource-consuming and requires specific expertise, which is not always available. To tackle these issues, in the context of the H2020 project RESCCUE (RESilience to cope with Climate Change in Urban arEas), a methodology to effectively prioritize adaptation measures against extreme rainfall-related hazards in urban areas has been developed. It follows a multi-phase structure to progressively narrow down the list of potential measures. It begins using less resource-intensive techniques, to finally focus on the in-depth analysis on a narrower selection of measures. It involves evaluation of risks, costs, and welfare impacts, with strong focus on stakeholders’ participation through the entire process. The methodology is adaptable to different contexts and objectives and has been tested in two case studies across Europe, namely Barcelona and Bristol.