Amid the accelerating rise in temperature worldwide, the number of summer heat patients continues to increase despite the nation's No. 1 rank in terms of ratio of heat shelters per area in Seoul. This study analyzed the effect of shuttle operations using the System Dynamics-GIS model to secure the mobility of cooling shelters for the vulnerable population in Seoul. To input into the System Dynamics model, spatial information consisting of the vulnerable population for each Dong in Seoul, cooling shelter (capacity, location), and DEM data were analyzed in GIS. By designing a stock-flow model based on the spatial input information, the pattern of decrease of the heat wave exposure rate according to the evacuation rate of the vulnerable was analyzed in time series. The scenarios consisted of not operating a shuttle bus (Scenario 0), operating a shuttle bus (Scenario 1), and efficient shuttle distribution with the operation (Scenario 2). The heat wave exposure rates of each scenario were 83.5%, 74%, and 59.58%. The heat wave exposure rate of the vulnerable group due to shuttle operations has decreased by as much as 23.92%, and this study’s results can serve as primary data when establishing policies related to shuttle operations.