An operational framework for flood risk assessment in ungauged urban areas is developed within the implementation of the EU Floods Directive in Greece, and demonstrated for Volos metropolitan area, central Greece, which is frequently affected by intense storms causing fluvial flash floods. A scenario-based approach is applied, accounting for uncertainties of key modeling aspects. This comprises extreme rainfall analysis, resulting in spatially-distributed Intensity-Duration-Frequency (IDF) relationships and their confidence intervals, and flood simulations, through the SCS-CN method and the unit hydrograph theory, producing design hydrographs at the sub-watershed scale, for several soil moisture conditions. The propagation of flood hydrographs and the mapping of inundated areas are employed by the HEC-RAS 2D model, with flexible mesh size, by representing the resistance caused by buildings through the local elevation rise method. For all hydrographs, upper and lower estimates on water depths, flow velocities and inundation areas are estimated, for varying roughness coefficient values. The methodology is validated against the flood event of the 9th October 2006, using observed flood inundation data. Our analyses indicate that although typical engineering practices for ungauged basins are subject to major uncertainties, the hydrological experience may counterbalance the missing information, thus ensuring quite realistic outcomes.