Migrations of most animal taxa are declining as a result of anthropogenic pressures and land-use transformation. Here, we document and characterize a previously unknown multi-country migration of Burchell's zebra Equus quagga that is the longest of all recorded large mammal migrations in Africa. Our data from eight adult female zebras collared on the border of Namibia and Botswana show that in December 2012 all individuals crossed the Chobe River and moved due south to Nxai Pan National Park in Botswana, where they spent a mean duration of 10 weeks before returning, less directly, to their dry season floodplain habitat. The same southward movements were also observed in December 2013. Nxai Pan appeared to have similar environmental conditions to several possible alternative wet season destinations that were closer to the dry season habitat on the Chobe River, and water availability, but not habitat or vegetation biomass, was associated with higher-use areas along the migratory pathway. These results suggest a genetic and/or cultural basis for the choice of migration destination, rather than an environmental one. Regardless of the cause, the round-trip, straight-line migration distance of 500 km is greater than that covered by wildebeest Connochaetes taurinus during their well-known seasonal journey in the Serengeti ecosystem. It merits conservation attention, given the decline of large-scale ecological processes such as animal migrations.