Originally known as Calabouço Airport, the history of the airport can be traced back to the early 1930s. Until that time, the few aircraft equipped with landing gear used the Manguinhos Airport. Seaplanes, which at the time operated the majority of domestic and international flights, used a terminal located at the Calabouço Point, an area known today as the Praça Marechal Âncora. Take-off and landings were made using an area of the Guanabara Bay then known as estirão do Caju (Caju water stretch). It was as a development of the terminal at the Calabouço Point that the Calabouço Airport was created.

In 1934, land was reclaimed from the sea to create the first runway of the airport with a length of 1,300 feet (400 m). In 1936, the runway was extended to 2,300 feet (700 m) and on 30 November, the airport was officially opened, being named Santos Dumont Airport. The first commercial flight arrived on the same day, a VASP Junkers Ju 52 aircraft flying from São Paulo–Congonhas.

Pan American World Airways and its Brazilian subsidiary Panair do Brasil opened their own terminal for seaplanes in 1937. It features architecture inspired by the Panamerican Seaplane Base and Terminal Building in Miami. It remained the headquarters of Panair do Brasil until the airline was forced to cease its operations in 1965. It is now the headquarters of the Third Regional Air Command of the Brazilian Air Force.

In 1938 the construction of a new passenger terminal began. It was a project led by the architects MMM Roberto (Marcelo, Milton and Mauricio Roberto Doria-Baptista) inspired in the Paris–Le Bourget Airport terminal. Its pioneering, modernist, architectural features caused it to become a Brazilian national landmark in 1998. It was only in 1945 that the terminal's construction was completed, which was interrupted by World War II. This building continues to be used to the present day, but only for arrivals.

Also in 1938, the runway was extended from 700 to 1050 meters to satisfy the demand for land aircraft.

In 1947, the runway was extended to 1,350 meters.

On 21 July 1953, within a law prescribing rules for the naming of airports, the name of the facility was officially and exceptionally maintained as Santos Dumont Airport.

On 21 May 1959 a formal agreement between Varig, Cruzeiro do Sul, and VASP created an air shuttle service (Portuguese: Ponte Aérea), the first of its kind in the world. This service operated between the Santos Dumont Airport and the São Paulo–Congonhas and comprised regular hourly departures, common check-in counter, and simplified tickets. The service was an instant success. Transbrasil joined the partnership in 1968. Starting in 1975 the service was operated exclusively by Varig's Lockheed L-188 Electra propjets. In 1999 this service came to an end because airlines decided to operate their own independent services.

With the gradual shift of international operations to the Galeão Airport, opened in 1952, the Santos Dumont airport lost its place as an international hub, and then lost its place as the most important domestic hub in 1960, when the capital of Brazil was moved to Brasília.

The airport handles only part of Rio's short-to-medium haul domestic air traffic, and part of its general aviation and military operations. The airport is famous for having some of the shortest runways on which some Boeing and Airbus aircraft can land. An idea of these operations is given in the 007–James Bond film Moonraker of 1979, in which a Lockheed L-188 Electra briefly appears taking-off from the airport.

The airport was heavily damaged in a fire on 13 February 1998, which kept the airport closed until 15 August 1998.

In March 2005, an ordinance restricted the airport's operations to domestic flights, general aviation, and air taxi. Among others, the main limitation centers on turboprop aircraft, with a maximum capacity of 50 seats on regular flights, with the exception of flights to Sao Paulo which operate without restriction.

On 26 May 2007, in time for the 2007 Pan American Games, a brand-new, modern extension of the original terminal was opened. This extension handles all departure operations, whilst the original terminal now handles all arrival operations. The new departures terminal increased the total capacity of the airport to 8.5 million passengers/year and added 8 passenger gates. It also introduced a one-of-a-kind climate control system, with the air conditioning installed in the floor to prevent obstruction of the view. The total area was increased from 19,000 m² to 61,000 m².

On 3 September 2009, the operational standards were adjusted; the airport would close between 23:00 and 06:00 hours, and the maximum number of flights per hour was reduced from 23 to 19, being one of the five airports with such restrictions in Brazil.

On 31 August 2009, Infraero unveiled a BRL152.2 million (US$80.2 million; EUR64.5 million) investment plan to upgrade Santos Dumont Airport, particularly the passenger arrivals terminal. The plan focused on the preparations for the 2014 FIFA World Cup, which was held in Brazil and Rio de Janeiro being one of the venue cities, and the 2016 Summer Olympics.