Jaguars (Panthera onca), like other apex predators, are highly susceptible to habitat loss and fragmentation given their low demographic potential and large habitat area requirements. Across their range, the Pantanal is considered critical for the jaguar’s long-term conservation. Here we provide the first multi-scale path selection function model for jaguars, and the first empirically-based movement model covering the entire Pantanal ecosystem. Out of eight investigated variables, six were related to jaguar habitat use in the Pantanal: terrain roughness, human population density, grassland, percentage of tree cover, flooded habitats and shrubland. The results of scale optimization revealed that jaguars responded primarily to landscape variables at broad scales (32 km) of habitat availability, with only one variable (grassland) influencing jaguar path selection at a finer scale (4 km). Jaguar habitat use was positively associated with flooded habitats and densely forested areas and negatively associated with grassland, terrain roughness, and human population density, with the latter having the strongest negative effect on jaguar movement. The prediction map suggested that only 9.3% of the total suitable jaguar habitat in Pantanal is protected by Conservation Units. Among the most suitable areas, the largest continuous habitats were located in the northwestern portions of the Pantanal, which corresponds to the interfluvial areas between Corixo Grande and Cuiaba rivers. Our results suggested that the implementation of already proposed North Pantanal Conservation Unit Mosaic in this area would be highly valuable for jaguar conservation. This study provides a foundation for future research to delineate and prioritize core areas and corridors for jaguars in the region.