Carex rupestris is an endangered and rare arctic-alpine element of the Western Carpathian flora. Given the geographically isolated and spatially restricted peripheral ranges of arctic-alpine species, there is a good chance that many species of conservation concern irreversibly disappear from the regional flora under the ongoing climate change. In this study, we gathered all existing data on the presence of C. rupestris and focused on its current and future distribution in the Western Carpathians. We found that although the distribution of the species is fragmented and scarce, C. rupestris occurs in several mountain ranges, in four distinct plant community types, which differ considerably in altitude, geological bedrock, and other habitat characteristics. In contrast to the relatively broad range of occupied habitats, C. rupestris shows a narrow temperature niche (mean annual temperature range 0.4–4.0 °C). Ensembles of small models based on climatic characteristics and local topography show that regardless of the climate change scenario (rcp2.6, rcp8.5), many current occurrence sites, mainly in the peripheral zones of the range, will face the excessive loss of suitable environmental conditions. It is expected that the Tatra Mountains will be the only mountain range retaining potentially suitable habitats and providing possible refugia for this cold-adapted species in the future. Such severe shrinkage of distribution ranges and associated geographic isolation raises serious concerns for the fate of the arctic-alpine species in the Western Carpathians.