The increasing risk of flooding in urban areas has led to many flood risk assessments. However, existing risk assessment methods are unable to select and reflect only the damage target and estimate a biased risk index due to data bias. Therefore, this study estimated flood risk index based on an indicator-based approach (IBA) using flood risk maps and grid data for 44 cities in South Korea. For each city, we used the overlapping grid data with the flood risk map. In addition, we divided the distribution of the data into 10 quantiles and scored the data according to each interval. Finally, the flood risk index was calculated based on entropy and Euclidean distance weights. Comparing the results between the estimated flood risk index and the flood damage data for 2019 shows an improvement over the existing methods. It is believed that the proposed method can accurately identify the flood risk, but also be used to support the decision-making process.