Abstract Permafrost covers a wide area of the Northern Hemisphere, including high-altitude mountainous areas even at mid-low latitudes. There is concern that the thawing of mountain permafrost can cause slope instability and substantially impact alpine ecosystems. However, permafrost in mountainous areas is difficult to observe, and detailed analyses have not been performed on its current distribution and future changes. Here, we show that the surface air temperature required to sustain Japan's mountain permafrost is estimated to decrease rapidly at present; most mountain permafrost in Japan is projected to disappear by the second half of the 21st century, and disappear very quickly in some places from approximately 2020–2030, regardless of climate scenarios. Our projections indicate that climate change has a considerable impact on mountain environments and that even if climate stabilization is achieved, Japan's mountain permafrost may almost disappear. It is important to consider measures to adapt to the changing mountain environment.