Weather changes such as rainfall can lower the efficiency of public transportation system. With upcoming light rail and BRT expansion in many cities, if municipalities cannot properly respond to the negative effects of weather changes on transit service, transit users cannot avoid experiencing inconveniences in their travels. This study analyzes the impact of rainfall on bus service in Seoul. To isolate the effect of rainfall, this paper adopted a mixed model in an attempt to control for various factors that might affect public transit service when it is raining. From the analysis, it appears that a rainfall makes bus transportation system especially inefficient during morning peak hours. With a 30mm rainfall per hour between 7 and 9 AM, the punctuality grows worse by more than 100 percent and the average speed becomes slower by 6km per hour. In future studies, it is desirable to directly control for confounding factors. Most of all, the analytical methods used in this study should be applied to a smaller spatial scale with a smaller unit of analysis. It would then be possible to develop a specific scheme to properly respond the weather changes and its effects on public transportation system.