Planted sugar cane farms covered some 3,796 acres (1,536 ha) that the government purchased for military use in the first week of September 1939 at a cost of $1,215,000.

Ramey AFB was home to a Strategic Air Command bombardment wing and housed a number of B-36 Peacemaker intercontinental bombers.

In the mid and late 1970s, the Ahrens Aircraft Corporation attempted to set up operations at former USAF industrial facilities at the airport in order to manufacture the Ahrens AR 404 regional airliner, a short takeoff and landing (STOL) turboprop aircraft, with financial incentives promised by the Puerto Rican government for development.

However, a subsequent government investigation over these incentives ensued and the project was cancelled after only two AR 404s were built at Rafael Hernández Airport.

In 2004, the Puerto Rico Ports Authority announced that it would be remodeling and expanding BQN to accommodate more flights and passengers.

On April 10, 2014, Lufthansa Technik announced the creation of a maintenance, repair and overhaul center (MRO) at the airport.

[citation needed] In the early 1990s, Carnival Airlines also operated the first intra-Puerto Rican jet service from the airport to Ponce with Boeing 727s as well as with wide body Airbus A300s.

North Cay Airways also provided passenger air service from San Juan at some time during the airport's history.

[25] In 2000, North American Airlines had reopened passenger service with a non-stop flight to New York JFK three times a week.

Boston-Maine Airways operating as Pan Am began jet service to Orlando Sanford International Airport in Florida and to Santo Domingo.

On June 2, 2008, Pan Am World Airways Dominicana restored service between the airport and Santo Domingo-Las Americas as well as to Punta Cana in the Dominican Republic.

The new service operates three to four times weekly and marks the airline's 13th route serving Puerto Rico from destinations in the U.S. and the Caribbean.

In the mid and late 1970s, the Ahrens Aircraft Corporation attempted to set up operations at former USAF industrial facilities at the airport in order to manufacture the Ahrens AR 404 regional airliner, a short takeoff and landing (STOL) turboprop aircraft, with financial incentives promised by the Puerto Rican government for development.

However, a subsequent government investigation over these incentives ensued and the project was cancelled after only two AR 404s were built at Rafael Hernández Airport.

In 2004, the Puerto Rico Ports Authority announced that it would be remodeling and expanding BQN to accommodate more flights and passengers.

On April 10, 2014, Lufthansa Technik announced the creation of a maintenance, repair and overhaul center (MRO) at the airport.

Since the airport was transferred from the U.S. Air Force and the General Services Administration (GSA) to Puerto Rico Port Authority in 1973, the south side has been the object of various disputes and competing political campaign promises by local elected officials and local political candidates.

Under the administration of Sila M. Calderón and Aníbal Acevedo Vilá, a master plan was conceived to turn the south side into an air cargo hub for the Caribbean, but local residents objected to the use of the south side for cargo rather than a modern passenger terminal.

A January 16, 2010, news report stated that the Federal Aviation Administration (FAA) approved a master plan to redevelop the Rafael Hernández Airport in Aguadilla that would involve an investment of $1 billion over the next 20 years.

In June 2021, an official plan of expansion was announced by the Puerto Rico Ports Authority and paid by the FAA.

[31] There are also plans to renovate the airport's facilities including bathrooms, relocating stores, adding jet bridges and more.