Construction was started by Philippine Commonwealth troops just after American forces landed at the present location on March 15, 1945.

When completed, the single runway was about 1,400 meters (4,500 ft) long aligned southwest to northeast.

On December 10, 2004, South Phoenix Airways announced their international flights to Sandakan and Kota Kinabalu in Malaysia, but it was eventually cut due to poor load of passengers.

Likewise, Asian Spirit commenced service to Sandakan on May 2, 2007, restarting Zamboanga's international operations.

[7] Due to the US-RP Agreement, the US Air force used the airport while the Balikatan military exercises were held in the city.

[11] Due to its potential as a key-areas in the BIMP-EAGA zone, there are plans to reinstate its international routes.

[12] Flights to Kota Kinabalu operated by PAL Express De Havilland Canada Q400s were to begin on March 31, 2020, but did not push through as travel restrictions due to the COVID-19 pandemic were enforced.

[15][16] There were plans in 2007 to transfer the airport to a 104-hectare (260-acre) lot located between Barangays Talabaan and Taluksangay, about 12.75 km (7.92 mi) from Zamboanga City.

[17] However, it was supported by the Philippine Chamber of Commerce and Industry with the purpose of converting the current property to a business district.

[18] The airport project, at its current form, will be located on a 175-hectare (430-acre) area in barangays Mercedes and Talabaan, 17 kilometers (11 mi) away from the city.

There are plans to extend the runway to 3,000 meters (9,800 ft), making it capable of receiving even bigger aircraft.

The runway is presently being shared between the airport and the Edwin Andrews Air Base (EAAB).

[15][16] The terminal houses a metal detector and an X-ray machine, both located at the main entrance of the airport and before entering the Pre-Departure Area.

[2] This article incorporates public domain material from the Air Force Historical Research Agency