The El Niño-Southern Oscillation (ENSO) can significantly affect the rapid intensification of tropical cyclones over the western North Pacific (WNP). However, ENSO events have various durations, which can lead to different atmospheric and oceanic conditions. Here we show that during short duration El Niño events, the WNP tropical cyclone rapid-intensification mean occurrence position migrates westward by ~8.0° longitude, which is caused by reduced vertical wind shear, increased mid-tropospheric humidity, and enhanced tropical cyclone heat potential over the westernmost WNP. The changes in these factors are caused by westward advected upper ocean heat during the decaying phase of a short duration El Niño. As super El Niño events tend to have short durations and their frequency is projected to increase under global warming, our findings have important implications for future projections of WNP tropical cyclone activity.