The jaguar (Panthera onca) is the largest felid in the Neotropics, and habitat fragmentation and conversion are severe threats for this species. We used empirical models to identify the suitable habitat and the functional corridors for jaguars to design a strategy to maintain connectivity in the Southern Mayan Forest, which spans the border of Mexico and Guatemala. We used Resource Selection Probability Functions to identify suitable habitat patches that were occupied by jaguars. Then, we used Step Selection Functions to directly measure movement probability given different landscape variables and to generate a resistance matrix to develop a model of habitat connectivity through Circuit Theory approach. Finally, we categorized the habitat patches and corridors to establish conservation and management priorities. Landscape variables that best described habitat use and movements of jaguars were similar. We propose that suitable habitat is maintained in large areas of primary forest, which are located at longer distances from deforested patches with relatively gentle topography. On the other hand, the functional connectivity exists through areas that include forest cover in a surrounding area within 240 m, and through areas with moderate to medium slopes or flat areas. We identified 27 habitat patches and 50 corridors for jaguars in the Southern Mayan Forest. However, we identified some gaps in the protection of these key habitats and corridors. Decision-makers in Mexico and Guatemala should encourage investment in specific sites for conservation, management programs, and habitat restoration to ensure the integrity of the entire Mayan Forest ecosystem.