Military use

The airport was built by the Japanese Navy about 1943, calling the military airfield Guamu Dai Ni (Guam No. 2) as part of their defense of the Marianas. After the island was recaptured by American forces in 1944, it was renamed Agana Airfield, due to the proximity of the town. After being repaired by Seabees of the 5th Construction Brigade in October 1944, the United States Army Air Forces Seventh Air Force used the airfield as a base for the 11th Bombardment Group, which flew B-24 Liberator bombers from the station until being moved to Okinawa in July 1945. With the reassignment of the heavy bombers, the 41st Photographic Reconnaissance Squadron flew long-range reconnaissance aircraft (F-5 Lightnings) from the field until January 1946.

After the war, the USAAF used the airfield for fighter defense of the Marianas (21st Fighter Group), (549th Night Fighter Squadron) until early 1947 and as a transport hub (9th Troop Carrier Squadron). In 1947, the USAAF turned over the airfield to the United States Navy, which consolidated its facilities with those at the closing Harmon Air Force Base in 1949, and operated Naval Air Station Agana until it was closed by the 1993 Base Realignment and Closure Commission.

Civilian use

Travel to Guam was restricted to military personnel with a security clearance until 1962. During these early years, a single Quonset hut served as Guam's air terminal. The lifting of this travel restriction spurred the development of the airport; its International Air Terminal opened in March 1967 and accommodated its first tour group from Japan two months later. Operations of the terminal were passed onto the Government of Guam's Department of Commerce in 1969. In 1975, the Guam International Airport Authority (GIAA) was created as a separate agency. After NAS Agana was closed in April 1995, GIAA took over the entire airport's operations.

A new passenger terminal building was opened in 1982, and the current, much larger terminal building was opened in phases between 1996 and 1998.

After a period of seasonal charters, the first regular flight to Mainland China from Guam was established in 2014. The United Airlines service to Shanghai Pudong International Airport began on October 29, 2014.

Project Hulo'

In July 2017, the A.B. Won Pat International Airport Authority launched its Vision Hulo' campaign, which includes around $167 million in capital improvement projects to help boost services and operation for the airport. The projects are set to increase the airport's passenger capacity, which already annually serves 3.55 million departing and transiting passengers. The projects include the relocation of bulky baggage screenings, additional security lanes, the expansion of parking spaces, and more.

A $110 million international arrivals corridor, the largest in the project, is the airport's newest capital improvement project. The third level corridor will finally put the airport compliance with federal regulations by the U.S. Transportation Security Administration in 2005, in response to 9/11, by separating arriving international passengers with departing passenger and allowing the airport to finally remove the semi-permanent barriers and reclaim full use of the concourse.

In the initial months of the COVID-19 pandemic in Guam, flights to and from Guam stopped, except for United Airlines, which maintained daily service to Honolulu and thrice-weekly service to Narita. A year later in April 2021, limited flights were being conducted by United Airlines, Philippine Airlines and Jin Air.