Satellite remote sensing has been used effectively to estimate flood inundation extents in large river basins. In the case of flash floods in mountainous catchments, however, it is difficult to use remote sensing information. To compensate for this situation, detailed rainfall–runoff and flood inundation models have been utilized. Regardless of the recent technological advances in simulations, there has been a significant lack of data for validating such models, particularly with respect to local flood inundation depths. To estimate flood inundation depths, this study proposes using a backpack-mounted mobile mapping system (MMS) for post-flood surveys. Our case study in Northern Kyushu Island, which was affected by devastating flash floods in July 2017, suggests that the MMS can be used to estimate the inundation depth with an accuracy of 0.14 m. Furthermore, the landform change due to deposition of sediments could be estimated by the MMS survey. By taking into consideration the change of topography, the rainfall–runoff–inundation (RRI) model could reasonably reproduce the flood inundation compared with the MMS measurements. Overall, this study demonstrates the effective application of the MMS and RRI model for flash flood analysis in mountainous river catchments.