The airport is located just north of the city's central business district, adjacent to the main campus of Upper Nile University.

Malakal is the smaller of two international airports in South Sudan.

The largest, Juba International Airport, lies approximately 521 kilometres (281 NM) to the south in the capital city of Juba.

As part of the United Nations Mission in Sudan (UNMIS), the airport was a major staging point for United Nation operations to South Sudan and will continue to do so under the new United Nations Mission in South Sudan (UNMISS) mandate.

[3] The airport resides at an elevation of 1,291 feet (393 m) above mean sea level.