The flood damage reduction studies have been performed by the channel improvement plan and the levee has mainly constructed with the freeboard concept. However, the freeboard concept might be an inappropriate choice as a safety factor of the levee because many uncertainties are involved in the procedure of the channel improvement plan studies. So, we considered the uncertainties In the discharge-probability, stage-discharge, and stage-damage functions and estimate the expected annual damage. The Monte Carlo technique for uncertainty analysis is used. As our results, the expected annual damage with uncertainty shows the larger value than without uncertainty. Since the expected annual damage with uncertainty already considers the safety factor it is the proper result. However, the expected annual damage without uncertainty does not consider the safety factor yet. Thus, if the expected annual damage without uncertainty considers the freeboard concept, it could be compared with the expected annual damage with uncertainty for the evaluation of the overestimation or underestimation of the levee construction.