Avian pox viruses (APVs) have been reported to cause infection in diverse avian species worldwide. Herein we report the first case of APV infection in a free-living bird, a subadult crested serpent eagle (Spilornis cheela), in Taiwan. In addition to the typical wart-like lesions distributed on the cere, eyelid, and face, there were also yellowish nodules below the tongue and on the hard palate. Phylogenetic analysis of the 4b core protein gene showed that the APV is very close to that found in white-tailed sea eagle (Haliaeetus albicilla) in Japan recently. Because both cases are located on the same major flyway for migratory birds, the impact of this virus with regard to the wild and migratory raptor species along the East Asian–Australasian Flyway and West Pacific Flyway requires immediate investigation.