The use of species distribution modelling under climate change to anticipate alterations in species’ habitats is a concern in ecological conservation. This research aimed to simulate the present suitable habitat distribution of three species that are rare and endemic to Pakistan and to analyse the possible climate change consequences on habitat suitability in the future (2050 and 2070). We projected potentially suitable habitat distributions using two shared socioeconomic pathways scenarios (SSPs 245 and SSPs 585). The potential distribution was modelled with MaxEnt using species presence-only data, and environmental variables. The modelling approach included seven climate-related variables in total. The model was validated using AUC, TSS, and Jackknife. For all species, the AUC score was >0.85. The present distribution of all three species has been significantly impacted by precipitationrelated factors (bio 14, bio 17, and bio 18). The temperature and topographic diversity also impacted the distribution. The potentially suitable habitat for Buxus papillosa and Rydingia limbata is projected to increase (39 % and 44 % respectively) in the 2050s under SSPs 245, and the potentially suitable habitat for Gentiana kurroo is projected to decrease (24%) in 2070s under SSPs 585. All species may expect appropriate habitats to expand or shrink, however, there will probably be a significant loss of native habitats. We recommend designating climate-change-affected places as conservation protection zones based on these results.