As a result of the Torrijos-Carter Treaties, on November 1, 1999, the air base was transferred to Panamanian control and converted into a civilian airport.

Like many of the military structures that passed into Panamanian hands and were given civilian use, part of the former air base attached to the airport became a mixed-use real estate development under the Panama Pacifico Special Economic Area, with the creation of the Panama Pacifico Special Economic Area Agency (APP), housing multinational companies such as 3M, Dell Technologies, VF Corporation, BASF, Caterpillar, among many others.

On August 1, 2014, ultra-low-cost airline VivaColombia became the first company to fly regularly to Panamá Pacífico, launching flights from Bogotá and Medellín.

[10] Starting in 2019, the Ecuadorian airline Aeroregional began operating a series of weekly charter flights between Quito and Panamá Pacífico, a route that has proven to be consolidated and has become a regular international destination.

[11] On July 28, 2022, the airport was reopened with the inauguration of the new passenger terminal and the resumption of commercial flights by Aeroregional, originating from Quito.