1946–1975

The airport was built by the colonial administration of the then Portuguese Timor in the aftermath of World War II. Construction began in 1946, and for the most part was carried out manually, with thousands of Timorese preparing the runway by hand.

The then Australian consul to the colony, Charles Eaton, who took up his post in January 1946, was a retired officer of the Royal Australian Air Force (RAAF). He had been involved in the RAAF bombing of Timor during the war. While serving as consul, he became an unofficial advisor to the colony on civil aviation matters. Soon after his arrival, the Governor, Óscar Freire de Vasconcelos Ruas, asked him to inspect the proposed site of the airport. On a subsequent visit to Australia, he lobbied the Chief of Air Staff and Director of Aviation of the RAAF to ensure that the airport was equipped with the best available technology.

In May 1947, the airport was opened. The persons invited to the opening ceremony included Resident C.W. Schuller, the head of the colonial administration in Dutch (West) Timor. He noted that Baucau was clearly designed as an international airport and rival to Penfui Airport in Kupang, Dutch Timor, which was then a staging post on flights between Australia and Java, but not yet officially an international facility. In late 1947, Ruas told Schuller that Lockheed Constellation aircraft operating the Darwin–Singapore–Hong Kong route were expected to stop in Baucau from 1 January 1948.

As of March 1948, no such stopovers had occurred, but plans for a Sydney–Darwin–Baucau–Shanghai–Hong Kong route were said by Schuller to be 'getting stronger'. Schuller also noted that local airline Transportes Aéreos de Timor (TAT) was expected soon to start flying Douglas DC-3 or Lockheed Hudson aircraft. However, subsequent reports by Dutch officials in 1948 and 1949 commented that at that time nothing had come of any of these plans.

Eventually, international flights did start serving Baucau Airport. During the rest of the Portuguese colonial era, the airport was the colony's main airfield. As of 1960, TAT was operating international flights between Baucau and Darwin, using small de Havilland airliners: either a Dove or a Heron. On 26 January 1960, the Heron flying one of these services crashed into the Timor Sea. In 1963, work on adapting the runway to make it capable of handling Boeing 707s was completed, although the airport was still not equipped with an instrument landing system.

As of 1964, TAT was using a chartered Trans Australia Airlines (TAA) Fokker F27 Friendship to operate the Baucau to Darwin flights, every week. In 1967, TAT was operating flights between Baucau and Oecusse, and between Baucau and Darwin, using two Doves. As of 1969, TAT was again using a chartered TAA F27 to fly the Baucau to Darwin route.

In the early 1970s, Baucau was the very last stop before Australia on the "hippy trail" from Europe. In 1974 and 1975, there were scheduled TAT domestic services between Baucau and Dili, and the Baucau to Darwin services flown for TAT by TAA had become thrice-weekly. After Cyclone Tracy devastated Darwin at the end of 1974, the flights between Baucau and Darwin were suspended for a time. Due to the political circumstances in Portuguese Timor, the very last such flight was on 7 August 1975.

An F27 was due to land in Baucau from Darwin on 11 August 1975, with Fretilin political party leader José Ramos-Horta aboard. On the evening of 10 August 1975, however, an opposing political party, the Timorese Democratic Union (Portuguese: União Democrática Timorense (UDT)), staged a coup d'état attempt in Dili and seized several strategic locations there, including Dili airport. An Australian TAT pilot, Roger Rudduck, who was involved in the coup, then sent radio messages for the UDT coup organisers from the Dili airport control tower to the Commander of RAAF Base Darwin and the Flight Services Unit at Darwin Airport. The messages advised that there had been a coup in Dili, and that it would be unsafe for the F27 to land in Portuguese Timor. The 11 August 1975 flight therefore never took off, with the intended result that Ramos-Horta was left stranded outside the colony.

As of late August and early September 1975, the airport at Baucau was under the control of the UDT. However, armed skirmishing was underway between the UDT and Fretilin to the west of Baucau.

1975–2000

On 9 December 1975, 156 Indonesian Air Force troops of the Kopasgat infantry and special forces corps, together with other Indonesian troops, parachuted into Baucau as part of the Indonesian invasion of East Timor. The objective of the Kopasgat troops was to capture the airport. The following day, 10 December 1975, Baucau fell to the Indonesians.