The jaguar Panthera onca, a threatened species in Brazil, is losing suitable habitat as a result of agricultural expansion and other forms of land conversion, especially in the Cerrado biome. In the current context of habitat loss and fragmentation, a network of protected areas is paramount for the conservation of this species. We aimed to identify jaguar conservation units in the Cerrado, and propose a ranking of priority areas for the species in this region. We used the maximum entropy algorithm to model habitat suitability for the jaguar in the Cerrado, with nine uncorrelated environmental variables and 106 non-autocorrelated presence-only records. We prioritized regions, using Zonation, and ranked jaguar conservation units according to their area, proximity to strictly protected areas, jaguar presence, and potential for connectivity. Circa 30% of the Cerrado is suitable for the jaguar. The most important variables affecting jaguar distribution are mean rainfall and land cover, with a high probability of jaguar presence in forest and savannah. We selected 31 high-priority jaguar conservation units, covering c. 174,825 km2 (8.5%) of the Cerrado. We emphasize the need for new protected areas and the promotion of sustainable development, as only 0.4% of the Cerrado (8,345 km2) has high environmental suitability for jaguars and < 1% of the area covered by jaguar conservation units falls within protected areas. Most jaguar conservation units identified here are relevant for habitat connectivity in Brazil, given their proximity to other critical areas for jaguar conservation in the Caatinga and the Amazon.