The Egyptian Vulture has been classified as ‘Endangered’ due to a rapid population decline in India and long term declines in Europe and Africa. Although the species has been reported to be declining in Eastern Europe, no quantitative assessment of the magnitude or the causes for population declines are available. We used monitoring data from the Balkan Peninsula to estimate changes in population size and extent of occurrence of Egyptian Vultures between 1980 and 2013. We quantified population trends in three countries (Bulgaria, Greece and the former Yugoslav Republic [FYR] of Macedonia) to assess whether population declines are similar within the Balkan range states. We found a rapid and consistent decline of the Egyptian Vulture population that was largely similar among the three countries (λ = 0.940 in FYR of Macedonia, 0.951 in Bulgaria, 0.920 in Greece). As a consequence of population declines, the breeding range of Egyptian Vultures has contracted and the population in the Balkan Peninsula has fragmented into six subpopulations separated by more than 80 km. Population declines may be driven by factors such as poisoning, electrocution, direct persecution and changes in food availability which operate at large spatial scales and affect birds both on breeding grounds as well as during migration and wintering. Because the relative importance of threats to the survival of Egyptian Vultures are poorly understood, there is a critical need for research into causes of mortality and potential conservation actions that may halt and reverse population declines.