A military airfield was opened at Olbia (then Terranova Pausania) in 1921, and a seaplane base was inaugurated close to the Isola Bianca harbour in 1927, although poor loads from the island on the flights to Ostia and Cagliari led to the service's stop in Terranova being discontinued in 1929. The airfield and seaplane base were targeted by Allied bombing in World War II, and the Germans opened Venafiorita airfield 7.2 kilometres (4.5 mi) south of the town. It was renamed Olbia in 1945.

Commercial flights gradually returned, and in 1963, the Olbia-based airline Alisarda was formed. It successfully expanded its route network, introducing jet flights in 1972, and it was renamed Meridiana in 1991. However, the introduction of jet aircraft necessitated the building of a larger airport nearer the city; the current airport was completed in 1974.

Following three years of work, a new terminal covering 42,000 square metres and capable of handling 4.5 million passengers per year, was unveiled on 6 June 2004. Costing a total of €81 million, the structure was designed by Willem Brouwer Architects and incorporated the original terminal building, which was developed into a 3000-square metre retail area. The new building has 40 check-in desks and fifteen boarding gates: five are equipped with jet bridges (Gates A1-A5) for Schengen passengers on full service carriers like Lufthansa or Air France, and occasionally by low cost airlines like Volotea or Vueling; one walking gate A6; and three non-Schengen bus gates (A7-A10) used by airlines like British Airways or Easyjet. Five further bus gates (B1-B6) exist on the lower floor for Schengen departures; these are used by ultra low cost carriers like Ryanair. The terminal contains a wide variety of shops and restaurants, a wine bar, a small art gallery, and indoor garden areas featuring local flora.

The airport also is home to the Tourist Management department of the University of Sassari.

From 3 February to 14 March 2020, the airport closed to passenger air traffic for the refurbishment and extension of the taxiways and runway. During this period, all flights arriving and departing were cancelled. The airport building remained in this period open to events of various kinds. The airport, which was initially scheduled to reopen on March 14, 2020, remained closed until June 2, as a result of the measures taken by the Italian authorities due to the COVID-19 pandemic in Italy. The airport reopened on June 3.