Understanding connectivity between migratory bird breeding and wintering grounds is essential for range-wide planning of conservation activities. We used GPS tracking to explore the migration of 28 ‘Endangered’ Greater Spotted Eagles, Clanga clanga from three remaining European breeding populations towards their wintering range, and to identify population and sex-specific patterns in selection of wintering sites. The tracked eagles wintered in three continents, 46% in Africa (mostly Eastern Sahel), 43% across southern Europe (mostly Greece) and 11% in Asia (the Middle East). Migratory connectivity was weak (rM = 0.16), and the population spread across the wintering range was large (1,917 km). The three studied populations differed in their migration strategy, with northerly, Estonian breeders all wintering in Southern Europe, and Polish and Belarusian breeders divided between Southern Europe and Africa. Migration strategy was different between Belarusian males and females, with males more likely to winter in Africa than Europe, and on average, migrating 2,500 km further south than females. Migration to Africa took longer, but was partly compensated by higher migration speeds. Greater Spotted Eagles wintered in wetland sites throughout their wintering range, with 15 of 29 birds wintering in internationally or nationally protected sites (including 12 Ramsar sites). Nearly a third of European winterers stayed in the same Greek national park, perhaps indicating a limitation of suitable sites in Europe due to wetland loss or degradation. This highlights the importance of protected wetlands to this species, but also shows their vulnerability to future wetland degradation. Only two of 14 wintering sites in Africa were under protection, showing a potential mismatch between protection of females and males in their wintering grounds.