Habitat loss is one of the main threats to wildlife, particularly large mammals. Estimating the potential distribution of threatened species to guide surveys and conservation is crucial, primarily because such species tend to exist in small fragmented populations. The Endangered huemul deer Hippocamelus bisulcus is endemic to the southern Andes of Chile and Argentina. Although the species occurs in the Valdivian Ecoregion, a hotspot for biodiversity, we have no information on its occupancy and potential distribution in this region. We built and compared species distribution models for huemul using the maximum entropy approach, using 258 presence records and sets of bioclimatic and geographical variables as predictors, with the objective of assessing the potential distribution of the species in the Valdivian Ecoregion. Annual temperature range and summer precipitation were the predictive variables with the greatest influence in the best-fitting model. Approximately 12,360 km2 of the study area was identified as suitable habitat for the huemul, of which 30% is included in the national protected area systems of Chile and Argentina. The map of potential distribution produced by our model will facilitate prioritization of future survey efforts in other remote and unexplored areas in which huemul have not been recorded since the 1980s but where there is a high probability of their occurrence.