Detecting and planning for ecosystem changes from climate and land-use alteration is limited by uncertainty about the current distribution of many species. This is exacerbated in remote areas like the Arctic, where the impacts of climate change are the strongest and where industrial exploration and development are expanding. Using remotely-sensed environmental information and known nest sites, we estimated the breeding distribution and habitat selection of the peregrine falcon (Falco peregrinus) throughout most of Nunavut, a massive northern Canadian territory (>1.8 M km2) encompassing ∼15% of the world’s tundra biome. Our results show that peregrine falcons selected features of prior known importance such as rugged topography, but also sites with higher than average summer temperatures, more productive land classes, lower mean elevations, and lower mean summer precipitation. Our model identifies several areas of high relative probability of peregrine occurrence, some of which were unrecognized to date. Some of these areas may be targets for future industrial developments and are located in an area where some of the fastest climate changes are expected. Our model will allow managers to identify the areas that could be the most critical for monitoring in the context of future development and climate change.