<p><i>Lilium&#xa0;polyphyllum</i>&#xa0;is a critically endangered medicinal plant found in the Himalaya. Due to the loss of habitat and unregulated collection, the species is facing a serious threat, and there is a need to restore the drastically reducing populations. Therefore, the present study was conducted to assess the populations in the Himalaya and identify suitable habitats of <i>L. polyphyllum</i> under projected climate change for conservation. Nine populations/sites (50 × 50&#xa0;m plot) were studied. The density of <i>L</i>. <i>polyphyllum</i> ranged from 0.23 to 2.50 Ind m⁻². <i>L. polyphyllum</i> density was very low, and it is positively correlated with the altitudinal gradient. In the current study, the MaxEnt algorithm, data on the occurrence of species, and environmental variables were used. Using the SSP370 and SSP245 climate scenarios of MIROC6 and BCC-CSM2-MR climate change models from the CMIP6 project for the period 2081–2100, species future distribution was predicted. MaxEnt predicted that the 2,42,573 km² area of the Hindu Kush Himalaya is conducive to the occurrence of <i>L. polyphyllum</i>. For both SSPs and GCMs, the distribution area expands as greenhouse gas concentrations rise. The areas where the probability of the species occurrence is highest can be used for in-situ conservation. Decision-makers and policymakers could develop effective management strategies by using the predicted species distribution maps.</p> Graphical abstract <p></p>