Selecting an optimum number of calibration sites for hydrological modeling is challenging. Modelers often spend a lot of time and effort on trial and error because there is no guide. We propose a novel entropy method to automate the selection of the optimum combination of calibration sites. To illustrate, the proposed entropy method is applied using discharge data from one river basin in Korea. First, different combinations of discharge-gauging sites were grouped based on the maximum information estimated by the entropy method. Then, a hydrological model was set up for the study basin and was calibrated by estimating optimal parameters using a genetic algorithm at the discharge-gauging sites. The calibration result confirmed that the model’s performance was best when it was calibrated using the site number and combination suggested by the entropy method. In addition, the entropy method was useful in reducing the time and effort of model calibration. Therefore, we suggest and confirm the applicability of the entropy method in selecting calibration sites for hydrological modeling.