1939–1975

The airport was built prior to World War II by the colonial administration of the then Portuguese Timor. Initially, it had an 800 m-long (2,600 ft) runway. It also soon became an operating base for Transportes Aéreos de Timor (TAT), which was founded in July 1939 as the colony's national airline.

In May 1939, the Portuguese government gave permission to Qantas to operate a Darwin to Dili flight. However, due to objections from the Japanese government, the Qantas services were postponed for more than a year. Eventually, in December 1940, the fortnightly Qantas Darwin to Batavia service was authorised to stop in Dili. The following month, Dili replaced Kupang as the stopover for Qantas's fortnightly Darwin to Singapore service. As compensation, Dai Nippon Airways of Japan was permitted to operate six trial flights from Palau to Dili between December 1940 and June 1941. In October 1941, the Japanese government announced plans to introduce regular air services between Tokyo and Dili, beginning the next month.

All of these flights were operated by flying boats, not by land-based aircraft needing to use a landing strip. At that time, Dili did not have the facilities required to handle Qantas's de Havilland D.H.86 land-based aircraft. The flying boat services have also been described as "pseudo-commercial", as they were of "negligible commercial importance", and used for "political penetration" in the lead-up to the Pacific War of 1941–1945. A radio room was set up in the Dili post office to communicate with the flying boats, using equipment supplied by the Australian Department of Civil Aviation.

Meanwhile, during 1940, TAT began flying a weekly land-based aircraft service between Dili and Kupang, using a de Havilland Dragon Rapide wet-leased from Koninklijke Nederlandsch-Indische Luchtvaart Maatschappij (KNILM), the airline of the then Dutch East Indies. Those services continued, again for political reasons, even after April 1941, by which time TAT was six months behind in paying the lease fees and salaries of the pilot and mechanic.

On 17 December 1941, soon after the beginning of the Pacific War, Dutch and Australian forces landed in Dili, with the objective of occupying the neutral territory of Portuguese Timor "... to defend against Japanese aggression ..." The 2nd Australian Independent Company took control of the airport. By 17 February 1942, the Allies had changed their stance, and arrangements had been made for their forces in Dili to hand over to a reinforced Portuguese garrison. On 20 February 1942, however, an Imperial Japanese Navy (IJN) invasion force landed to the west of the airport and captured it by 11:00 am. The radio equipment at the Dili post office was later smuggled out, to the 2nd Australian Independent Company, which by then had retreated to Timor's central mountains. Subsequently, the Imperial Japanese Army Air Service (IJAAF) used the airport as a military airfield, and between June 1942 and August 1944, it was bombed by Allied aircraft.

By the end of the Pacific War, the airport was disused and overgrown. Japanese forces continued to occupy it until 11 September 1945, when the garrison at Dili officially surrendered.

In post-war Portuguese Timor, Baucau Airport, which was opened in 1947, and was and still is equipped with a much longer runway, became the colony's main airport, including for international flights. Dili airport was used for domestic services.

As of 1969, TAT was flying from Dili to six other places in the colony.

In 1974 and 1975, TAT operated scheduled domestic services from Dili to Atauro, Baucau, Maliana, Oecusse and Suai. The company was also flying between Dili and Kupang in West Timor, Indonesia, once a week, using a Douglas DC-3 chartered from Merpati Nusantara Airlines.

1975–1999

During the Indonesian occupation after 1975, the airport at Baucau was placed under the control of the Indonesian National Armed Forces, and was closed to civilian traffic, although at least nominally it remained accessible to large civilian airliners. Dili airport became the territory's principal civilian airport.

In 1978, the Indonesian administration started work on rebuilding Dili airport, which it renamed as Comoro Airport (Indonesian: Bandar Udara Komoro). The work included the construction of a new passenger terminal building (without any custom, immigration and quarantine (CIQ) facilities), and the lengthening of the runway to accommodate Fokker F28s. In October 1978, Indonesia's State-owned flag carrier, Garuda Indonesia, inaugurated a Jakarta–Dili–Jakarta service. The full itinerary, which, initially, was flown three times a week, was Jakarta–Yogyakarta–Denpasar/Bali–Dili–Kupang–Denpasar/Bali. Tickets could be sold only to passengers who had a 'letter of transit' approved by a 'proper authority'. The leg from Jakarta to Denpasar/Bali was operated by a McDonnell Douglas DC-9, and that from Denpasar/Bali to Kupang by a Fokker F28. A connecting flight from Denpasar/Bali back to Jakarta was flown by a Douglas DC-8.

The rebuilding work at the airport was completed in 1981.