In the Indian Trans-Himalaya, Pallas’s cat Otocolobus manul is reported exclusively from Ladakh, Himachal Pradesh, Uttarakhand and Sikkim. In Ladakh, it has been reported primarily from the south-east, with no prior evidence of its occurrence in the north. In this study, we documented the first record of Pallas’s cat in the Karakoram Wildlife Sanctuary in the Nubra Valley, northern Ladakh. We identified the species based on the non-invasive genetic analysis of a morphologically ambiguous scat sample collected during a study on dietary patterns of sympatric carnivores. DNA-based species identification confirmed the presence of Pallas’s cat. We also identified prey remains, of pika Ochotona spp. and Himalayan marmot Marmota himalayana, in the scat. Our record extends the known range of Pallas’s cat into northern Ladakh and adds a new mammal species to the documented fauna of the Karakoram Wildlife Sanctuary. We recommend a comprehensive assessment of distribution, population, diet, habitat and potential threats to this elusive species to ensure its long-term survival in this landscape.