[4] It remained a spartan outpost until the Vietnam War in the 1960s when it became a base for a C-130 unit of the U.S. Air Force.

It replaced the now closed Lahug Airport (now the site of Cebu IT Park) which could no longer be expanded due to safety and physical problems.

[6] On April 23, 2014, the Department of Transportation and Communications awarded the operations and maintenance of MCIA to a consortium of the Philippine Megawide Construction Corporation and Bangalore-based GMR Infrastructure.

[8][9][10] On June 29, 2015, President Benigno Aquino III led the ground-breaking rites at the site of the old Philippine Air Force base in Lapu-Lapu City which had been demolished to give way for the Terminal 2 construction.

[19] On November 12, 2013, the world's longest and heaviest aircraft, the Antonov An-225 Mriya, landed at MCIA from the Zagreb International Airport in Croatia for the first time in the Philippines.

It delivered a 180-ton replacement transformer from the Croatian energy company KONČAR for the First Gen Corporation's power plant in Batangas City.

[20] According to First Gen President Francis Giles Puno, MCIA had been inspected by Antonov Airlines, the owner of the Antonov An-225 aircraft, as the most viable option for their aircraft, "after considering the combination of airport, onward land transport and sea freight.

"[21] Philippine Airlines offered non-stop flights to Los Angeles, the longest route from MCIA, from March 2016 to May 2017.

[25] On October 30, 2024, it fully acquired GMCAC for ₱7.76 billion, thereby completely taking over the operations of MCIA.

[30] President Rodrigo Duterte inaugurated the newly rehabilitated Terminal 1 on January 19, 2020, increasing its capacity to 11.7 million passengers.

[32] Construction began on January 22, 2016, and was inaugurated by President Rodrigo Duterte on June 7, 2018, before opening to passengers on July 1.

Terminal 2 won an award for the category "Completed Buildings – Transport" at the World Architecture Festival in 2019.

[34][35] Occupying an area of 65,500 square meters (705,000 sq ft), the terminal has four check-in halls with 48 check-in counters in the departures area expandable to 72, seven jet bridges expandable to 12, 12 escalators, 15 elevators, duty-free shops, and a departure lobby.

[28] The terminal's modular design allows for progressive expansion, with a fundamental building block structured for maximum adaptability to future development.

However, due to the aftermath of Typhoon Odette, it was used for both domestic and international flights from January 16, 2022, until most parts of Terminal 1 were fully repaired by June.