In the early 1920s, the Spanish navy acquired a large plot of land near Santiago de la Ribera, on the Mar Menor, between the Cartagena-Alicante road and the sea, in a place which combined superb weather conditions with a perfect location for seaplane activity. In 1927, the first designs were drawn up for the construction of the air-sea base and work commenced the following year. Hangars, classroom buildings, accommodations, a power plant, blocks and warehouses were built and wells were drilled to provide drinking water. Tanks, a hangar at one end of the field to house a SCA-type dirigible, a hydrogen factory and a small port were also constructed.

In 1929, the training organised by commercial flight services at the army and navy aerodromes opened the facilities at San Javier and Los Alcázares (an army-navy base established in May 1915 to the south of the town) to civil traffic. At that time, flight activity at Los Alcázares focused on the retraining of pilots as seaplane crews. In 1920, during a course, the Basic Pilot School was established there, as was the Air Combat and Bombing School in 1921.

In early 1932, essential work was being completed to make the San Javier air base usable, following which the Aeronautics services, which would be permanently based at San Javier, began to be transferred from Barcelona.

Opening to commercial air traffic

In 1963, a report by the 2nd Commission of the Provincial Tourist Assembly outlined the need to request the Air Ministry to open the San Javier and Alcantarilla airbases to commercial traffic. The General Air Academy was willing to receive commercial traffic at the San Javier airbase whenever it did not coincide with other flights. In addition, the commercial traffic required a number of facilities and services which the San Javier air station did not have and these had to be provided. Finally, on 20 July 1964, San Javier air station was officially opened to civil traffic.

Opening up to commercial air traffic also made it necessary to improve facilities in the manoeuvring area and, on 6 May 1965, a decree authorised the expansion of runway 05-23 to 2,300 metres in length. Some months later, the restoration and conditioning of the parallel taxiway was carried out and, in May 1966, work began on the aircraft parking area, the terminal and an access road from the Santiago de la Ribera - Los Alcázares motorway. Once the work was completed, San Javier Airport was opened to domestic and international passenger traffic on 17 May 1967. On 1 November 1968, it received its first scheduled flight from Madrid and, later, daily flights to Barcelona and on alternate days to Almería began.

To make it possible to receive international flights, the Cartagena Customs Offices were set up at San Javier Airport in March 1969, with a large room for the handling travellers, their possessions and luggage.

In the 1970s, improvements were carried out on the access road to the terminal and car park; a non-directional beacon and a VASIS were installed; the aircraft parking apron was extended, runway 05-23 was reinforced and a firefighting building was constructed.

In 1987, the offices of the Main Customs Administration of Murcia were enlarged at San Javier airport to allow the export of all kinds of products.

In the early 1990s, various building works were carried out to equip the airport with a passenger terminal building 3,500 square metres in area, enough to handle four flights simultaneously. In June 2004, the terminal was expanded to provide an additional 1,100 square metres in its arrivals area. In 2006 the departures area was enlarged to have more check-in desks and a renovated departures lounge, and the aircraft parking apron was equipped with capacity for 11 commercial aircraft and 10 general aviation aircraft. In 2011 the airport's second runway was opened, intended for military use, so that the existing runway can be used during the mornings for civil flight operations, except for specific restrictions.