The Endangered Kashmir musk deer Moschus cupreus is a conservation priority species facing population decline as a result of habitat loss and illegal hunting for its musk pod. Effective conservation requires identifying habitats that support the species’ survival and persistence. We used sign survey and camera-trap data with single-species occupancy modelling to examine the environmental factors influencing the species’ habitat use in Pattan Valley, Himachal Pradesh, and Govind Pashu Vihar National Park, Uttarakhand, India. We deployed a total of 43 camera traps and surveyed 54 trails in Pattan Valley, and had 23 camera traps and 43 trails in Govind Pashu Vihar National Park. The results indicate that M. cupreus occupies conifer forests (Pinus wallichiana, Picea smithiana, Abies spectabilis and Cedrus deodara, intermixed with Betula utilis) at 2,946–4,418 m in Pattan Valley, and mixed forests (P. wallichiana, P. smithiana, C. deodara, B. utilis, A. spectabilis, Taxus wallichiana and Quercus semecarpifolia) at 2,145–3,641 m in the National Park. Elevation and conifer forests had positive influences on the occupancy and detection probability of Kashmir musk deer in Pattan Valley, similarly mixed forests and elevation had positive influences on occupancy and detection probability, respectively, in Govind Pashu Vihar National Park. Contrarily, supporting model suggests that conifer forests have a negative influence on detection probability of Kashmir musk deer in the National Park. As high-altitude forested areas are vital habitat for M. cupreus, there is a need to improve protection and minimize anthropogenic disturbance in these areas. Our findings will aid wildlife managers in conservation planning and help inform management decisions for this species.