The phenology and routes of long-distance migrations of European Nightjars are well described for Western European individuals migrating within the East Atlantic and Mediterranean flyways, while little is known about populations from other parts of the Eurasian breeding range. We describe the route choice and timing of European Nightjars breeding in eastern Mongolia, migrating within the Asia–East Africa flyway to reach wintering destinations in South-East Africa. After covering about 15,000 km during autumn migration, Mongolian nightjars arrived 1 month later in their wintering grounds compared to nightjars breeding in Western Europe. A similar difference was also observed in the timing of their arrival back at their respective breeding grounds illustrating the differences in timing of migration events between the two populations. We identify the steppes of Central Asia and the savannah of the Horn of Africa and Eastern Africa as key stopover zones for nightjars associated with the crossing of an ecological barrier formed by the deserts and mountains of the Iranian Plateau and the Arabian Peninsula.