Urban flood damage is caused by various and complex effects such as inland flood and external water flooding, so research on this is necessary. This study presented a rainwater pumping station operation technique that can suppress the rise in water levels in discharge rivers based on rainfall and pump operation scenarios in order to reduce inland water flooding and simultaneously consider external water levels. The research method used genetic algorithm (GA) optimization techniques to calculate the optimal operating level for each pump, and based on this, an operating scenario was created to minimize pump operation. In addition, after constructing a rainfall scenario based on the probability rainfall in Seoul, an optimal pump operation technique that can reduce the external water level while minimizing the inundation of domestic water was proposed. The results of the study showed that as the rainfall intensity increases, the flooding increases and the peak depth of the runoff increases. In addition, as the pumping scenario changes from 1 to 11, the number of pumping operations decreases, which reduces the drainage volume of the pumps, which increases the flooding.