The objective of this study is to evaluate the appropriateness of methodology for designing urban sewer system using a rational method-based model, Makesw and an urban runoff model, SWMM. The Gunja basin was selected as a study area and precipitation, runoff, vegetation, soil, imperviousness data were used to estimate floods. The appropriateness of methodology was evaluated based on comparison analysis between floods estimated from Makesw and SWMM. The comparison analysis was conducted between floods estimated from Makesw and SWMM, which were simulated using design rainfall and measured rainfall from past inundation events. The comparison results showed that in the case of design rainfall, the rational method-based floods were larger than that based on SWMM in all main lines. However in several branch lines, the rational method-based floods were smaller than thoes based on SWMM. In addition, for the case of measured rainfall from past inundation events, it was easily to find the main and branch lines where the rational method-based floods were smaller than SWMM based ones. Especially, the lines where rational method-based floods were underestimated, were mostly main, 1st, 2nd lines. It was concluded that the rational method-based results were not conservative. Based on rational method (steady flow analysis) and SWMM (unsteady flow analysis), the more conservative results the method provides, the more highly it is recommended to use in designing an urban sewer system.