Knowledge about population attributes, current geographic distribution, and changes over predicted climate change for many threatened endemic vascular plants is particularly limited in arid mountain environments. Primula boveana is one of the rarest and threatened plants worldwide, surviving exclusively in Saint Catherine Protectorate in the Sinaic biogeographic subsector of Egypt. This study aimed to define the current state of P. boveana populations, predict its current potential distribution, and use the best-model outputs to guide in field sampling and to forecast its future distribution under two climate change scenarios. The MaxEnt algorithm was used by relating 10 occurrence-points with different environmental predictors (27 bioclimatic, 3 topographic, and 8 edaphic factors). At the current knowledge level, the population size of P. boveana consists of 796 individuals, including 137 matures, distributed in only 250 m2. The Canonical Correlation Analysis (CCorA) displayed that population attributes (density, cover, size index, and plant vigor) were positively correlated with elevation, precipitation, and pH. Based on the best-fitting model, most predicted suitable central sites (69 km2) of P. boveana were located in the cool shaded high-elevated middle northern part of St. Catherine. Elevation, precipitation, temperature, and soil pH were the key contributors to P. boveana distribution in Egypt. After field trips in suitable predicted sites, we confirmed five extinct localities where P. boveana has been previously recorded and no new population was found. The projected map showed an upward range shift through the contraction of sites between 1800 and 2000 m and expansion towards high elevation (above 2000 m) at the southern parts of the St. Catherine area. To conserve P. boveana, it is recommended to initiate in situ conservation through reinforcement and reintroduction actions.