Effects of climate change on the worst case scenario of a storm surge induced by a super typhoon in the present climate are investigated through the case study of Typhoon Haiyan. We present the results of our investigation on super-typhoon Haiyan by using a super high resolution (1 km grid) regional model that explicitly handles cloud microphysical processes. As the parent model, we adopted the operational weekly ensemble experiments (60 km grid) of the Japan Meteorological Agency, and compared experiments using sea surface temperatures and atmospheric environmental parameters from before the beginning of anthropogenic climate change (150 years ago) with those using observed values throughout the typhoon. We were able not only to represent the typhoon’s intensity but also to evaluate the influences of climate change on worst case storm surges in the Gulf of Leyte due to a typhoon with high robustness. In 15 of 16 ensemble experiments, the intensity of the simulated worst case storm in the actual conditions was stronger than that in a hypothetical natural condition without historical anthropogenic forcing during the past 150 years. The intensity of the typhoon is translated to a disaster metric by simulating the storm surge height by using a shallow-water long-wave model. The result indicates that the worst case scenario of a storm surge in the Gulf of Leyte may be worse by 20%, though changes in frequency of such events are not accounted for here.