Raptors play a unique role in ecosystem services and are regarded as effective indicators of ecosystem health. In recent years, varieties of anthropogenic factors have threatened the majority of raptor species worldwide. Nepal is considered a global hotspot for threatened and declining raptor species, but there is limited information on the direct human threats to the raptor populations living in the country. In this paper, we identify important anthropogenic threats to raptors in Nepal based on raptor mortality data collected by powerline surveys and from monitoring of GPS-tagged raptors, complete various reports, and social media. We found that powerlines, poisoning, and persecution, mainly shooting, are significant threats to raptors in Nepal that were largely overlooked previously. We report 54 electrocuted raptors affecting eight species, 310 poisoned raptors of 11 species, and five persecuted raptors of four species; among them vultures are the most affected (>88%). Based on our findings, to safeguard the future of Nepal’s raptors, we propose the retrofitting of power poles and the use of flight diverters on powerlines in the most affected areas to reduce raptor interactions with powerlines, as well as an effective conservation education programme to prevent the use of unintentional poisoning.