Cities are complex socioecological systems that are particularly vulnerable to the impacts of climate change and are also exposed to other trends, such as urbanization and population aging. Due to the changing climate, days with extreme temperatures are expected to become more numerous, which is particularly important for urban areas, where the urban heat island phenomenon is observed. This study presents an example of a spatially explicit potential climate change impact assessment of heatwaves integrating both science and stakeholder participation for three large Czech cities (Prague, Brno, and Pilsen). Stakeholder participation exercises were used to prioritize climate change risks, provide impetus and opportunity for knowledge co-production, and support adaptation planning. Potential climate change impacts of heatwaves in the three Czech cities for the current baseline (1981–2010) and for the future (2021–2040) using Representative Concentration Pathways (RCPs)—RCP 4.5 and RCP 8.5, were mapped at two levels describing “in-city” and “inter-city” comparison. When comparing the potential impact of heatwaves across the three cities (“inter-city”), the most affected city is Brno, with 10.5% of its area in the very high impact category for the baseline and both RCPs. The “in-city” comparison shows the differences between the baseline and future scenarios of each city. The assessment of heatwaves’ impacts was further used to support urban adaptation planning.