Climate change has severely impacted many species, causing rapid declines or extinctions within their essential ecological niches. This deterioration is expected to worsen, particularly in remote high-altitude regions like the Himalayas, which are home to diverse flora and fauna, including many mountainous ungulates. Unfortunately, many of these species lack adaptive strategies to cope with novel climatic conditions. The Red Goral (Naemorhedus baileyi) is a cliff-dwelling species classified as “Vulnerable” by the IUCN due to its small population and restricted range extent. This species has the most restricted range of all goral species, residing in the temperate mountains of northeastern India, northern Myanmar, and China. Given its restricted range and small population, this species is highly threatened by climate change and habitat disruptions, making habitat mapping and modeling crucial for effective conservation. This study employs an ensemble approach (BRT, GLM, MARS, and MaxEnt) in species distribution modeling to assess the distribution, habitat suitability, and connectivity of this species, addressing critical gaps in its understanding. The findings reveal deeply concerning trends, as the model identified only 21,363 km2 (13.01%) of the total IUCN extent as suitable habitat under current conditions. This limited extent is alarming, as it leaves the species with very little refuge to thrive. Furthermore, this situation is compounded by the fact that only around 22.29% of this identified suitable habitat falls within protected areas (PAs), further constraining the species’ ability to survive in a protected landscape. The future projections paint even degraded scenarios, with a predicted decline of over 34% and excessive fragmentation in suitable habitat extent. In addition, the present study identifies precipitation seasonality and elevation as the primary contributing predictors to the distribution of this species. Furthermore, the study identifies nine designated transboundary PAs within the IUCN extent of the Red Goral and the connectivity among them to highlight the crucial role in supporting the species’ survival over time. Moreover, the Dibang Wildlife Sanctuary (DWLS) and Hkakaborazi National Park are revealed as the PAs with the largest extent of suitable habitat in the present scenario. Furthermore, the highest mean connectivity was found between DWLS and Mehao Wildlife Sanctuary (0.0583), while the lowest connectivity was observed between Kamlang Wildlife Sanctuary and Namdapha National Park (0.0172). The study also suggests strategic management planning that is a vital foundation for future research and conservation initiatives, aiming to ensure the long-term survival of the species in its natural habitat.