Estimating flood hazard, vulnerability, and flood risk at the household level in the past did not fully consider all relevant parameters. The main objective of this study is to improve this drawback by developing a new comprehensive and systematic methodology considering all relevant parameters and their weighting factors. This new methodology is applied to a case study of flood inundation in a municipal area of Nan City in the Upper Nan River Basin in Thailand. Field and questionnaire surveys were carried out to collect pertinent data for input into the new methodology for estimating flood hazard, vulnerability, and risk. Designed floods for various return periods were predicted using flood simulation models for assessing flood risk. The flood risk maps constructed for the return periods of 10–500 years show a substantial increase in flood risk with the return periods. The results are consistent with past flood damages, which were significant near and along the riverbanks where ground elevation is low, population density is high, and the number of household properties are high. In conclusion, this new comprehensive methodology yielded realistic results and can be used further to assess the effectiveness of various proposed flood mitigation measures.