After critical facilities were completed in 2006, the current airport replaced the smaller Merowe Town airport 3 kilometres (1.9 mi) to the west.

[3] The new Merowe airport has hosted Sudanese Air Force jet fighters, but does not host any full time units stationed.

[4] The airport was attacked during the 2023-2024 War in Sudan, where RSF militias captured Egyptian soldiers who were serving joint military exercises with their Sudanese counterparts.

[5] Later, on 27 April 2024, the SAF claimed to have shot down three drones targeting the airport.

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