The sex ratio is an important concept in estimating population demography, and such data could contribute to both theoretical research and conservation. Although numerous studies have analyzed the sex ratios of raptors in the wild, few studies have focused on the sex ratios of raptors in wildlife rehabilitation facilities. Here, we report the results of polymerase chain reaction (PCR)-based sex identification of raptors brought to the Beijing Raptor Rescue Center in 2018–2020. This rescue center is located in eastern China, on a major migratory route for raptors in East Asia. We identified the sex of 646 individuals (belonging to 29 species) using two sets of primers, and analyzed the sex ratios of five species with a sample size >30 individuals. Generally, the sex ratios differed among species: the sex ratio of Eurasian Kestrels (Falco tinnunculus) was skewed toward males (P = 0.006), while the sex ratio of Eurasian Sparrowhawks (Accipiter nisus) was skewed toward females (P = 0.024). The sex ratio of Long-eared Owls (Asio otus) tended to be female-biased (P = 0.058). There was no significant bias of sex ratio in Oriental Scops-Owls (Otus sunia) or Amur Falcons (Falco amurensis). We discussed several possible reasons that could drive the biased sex ratios of raptors brought into rehabilitation centers. Our findings could be helpful for future studies on sex identification of raptors and conservation efforts.