The Natura 2000 network of protected areas is the backbone of species conservation in the European Union. We investigated whether Austrian-hatched white-tailed eagles (Haliaeetus albicilla) make particular use of this multinational network during their natal dispersal, and what habitats were of importance to the eagles. We analyzed the utilization distribution of 907,466 GPS locations from 38 dispersing white-tailed eagles using a dynamic Brownian Bridge Movement Model. Eagles ranged over a huge area of central-eastern Europe. Natura 2000 sites overlapped with 67% of the resulting 50% isopleth; i.e., a high probability of utilization of Natura 2000 areas by white-tailed eagles was found. White-tailed eagles used wetlands, waterbodies, and deciduous forests adjacent to wet habitats disproportionately often. Coniferous forests and settlements were avoided. Anthropogenically caused mortalities hardly occurred within Natura 2000 sites. Our study suggests that the Natura 2000 network is a crucial tool for conserving the white-tailed eagle. This top predator is an ambassador for the Natura 2000 idea during all life stages, and should continue to be a conservation priority of the network.