In recent decades, extreme storm events due to climate change have frequently occurred worldwide, a few of which have even occurred consecutively; we class such rainfall events as mega events. That is to say, if the inter-arrival time between rainfall events with a 100-year frequency is less than the IETD (Inter-Event Time Definition), the event can be considered a mega event. Therefore, the aim of this study was to implement flood inundation analysis using the hypothetical mega event from two consecutively occurring events of 100-year frequency, and select the optimal shelters using a developed method for minimizing casualties from floods. The Gyeongan stream basin, which is a tributary of the Namhan River in Korea, was selected as the study area. This study calculates mega flood discharge using the SSARR (Stream Synthesis and Reservoir Regulation) model, and conducts a flood inundation analysis of mega floods via the level pool method and the HEC-GeoRAS model. An inundation map was constructed, and the inundated area was classified into three zones and five administrative districts. Sixteen shelters were selected as candidates based on the criteria of the local government safety management plans and the Guidelines for Establishing the Disaster Relief Plan of 2013. To evaluate the candidates for evacuation in each district, we selected seven evaluation indicators from the shelter criteria of several countries, and calculated the weights of the indicators using the Analytic Hierarchy Process (AHP) method. As a result, four optimal shelters were selected in the study area. The results of the study can be used as the basic information for analyzing mega natural disaster events and inundation, and for establishing evacuation shelters, which are one of the non-structural flood protection measures.