The center was occupied by Kitty Hawk Aircargo, which had a hub at Fort Wayne until October 30, 2007, shortly after the carrier filed for Chapter 11 bankruptcy.

The former Kitty Hawk hub is now used by several aviation and non-aviation companies including Logistics Insight, FedEx Express, and Spinach Ball.

[7] The airport was built at a cost of $10 million as a United States Army Air Corps base just before World War II.

A coalition of city business interests arranged to purchase a series of contiguous land parcels outside of Fort Wayne, demolish the existing structures, and present a unified parcel to the War Department in a short enough period to meet a competitive deadline for the Development of Landing Areas for National Defense (DLAND) initiative while preserving civilian access to the existing Paul Baer Municipal Airport (now Smith Field) on the north side of the city.

The original airport had been named for Baer while he was still living, but he had since died in a seaplane accident in Shanghai while carrying mail and passengers for the China National Aviation Corporation.

A large number of ground and air squadrons trained at the facility before deployment to the European and Asiatic-Pacific Theaters of operations.

After the base was transferred to temporary inactive status, the city of Fort Wayne bought the airport from the federal government's General Services Administration for one dollar, renaming it Fort Wayne Municipal Airport in 1946, though colloquially the entire complex was still referred to as Baer Field, a practice reinforced by the reactivation of the base as Baer Field for military purposes in 1951.

The new permanent terminal had an air traffic control tower, an observation deck, and the "Look-Out Dining Room" restaurant with views of the ramp below.

In 1981, Baer Field's 1953 terminal building was modernized and expanded with features like jetways to handle increased traffic brought on by the Airline Deregulation Act.

Between 1994 and 1997, the terminal was again expanded, with design by MSKTD & Associates, Inc. Other improvements included runway upgrades and the Air Trade Center on the southwest side of the property.

Turboprops such as the Saab 340, Beechcraft 1900, ATR 72, and Dash 8 also continued to play a role for flights to destinations such as Milwaukee, Pittsburgh, Cleveland, and Detroit, occasionally alongside larger jets such as the DC-9, Fokker 100, and Boeing 737 on the same routes.

Demand for the flights reached the point where airport management bought the on-site Days Inn to make room for more parking.

In January 2007, a modernized 210 feet (64 m) air traffic control tower was opened on the south side of Fort Wayne International Airport, at a price of $9.7 million.

At one time, Allegiant also offered service to Fort Lauderdale from the airport and served Phoenix and Las Vegas before late 2008 as well.

However, the Phoenix and Las Vegas suspensions were ultimately temporary as Allegiant began adding more fuel-efficient Airbus A319 aircraft in 2013.

In the cases of both Cleveland and Cincinnati, the service discontinuation was part of broader hub cutbacks at both Continental and Delta that affected many other airports.

However, this service was unsuccessful due to local passenger preference for LaGuardia Airport and United’s 2018 decision to reduce Newark flying to many small markets.

Today Fort Wayne is served by four carriers: Allegiant Air, American Eagle, Delta, and United Express.

These three flights boosted the merged airline's departures from Fort Wayne by a third over the previous schedule, provided the airport's first route to the northeastern US since deregulation, and offered an additional gateway to the southeastern US and the Caribbean.

American remained committed to the airport, and continues to serve Charlotte, Chicago, and Dallas/Fort Worth multiple times daily.

[1][18] The runway is large enough to accommodate the NASA Space Shuttle orbiter, Airbus A380, Boeing 747, and military air mobility and aerial refueling aircraft such as the C-5 Galaxy, C-17 Globemaster III, KC-135 Stratotanker, KC-46A Pegasus, and KC-10 Extender.

[1][18] In the year ending August 6, 2018 the airport had 35,397 aircraft operations, average 97 per day: 47% general aviation, 36% air taxi, 16% airline, and 1% military.

The previous car rental lot was modified into a dedicated drop-off and pick-up point for taxis and hotel shuttles.

[21] The new facility, which replaced previous FBO Atlantic Aviation, offers a full range of services to private aircraft owners.

Fort Wayne Aero Center also supplies Avfuel-branded aviation fuels and deicing services to both private and commercial airline customers.

A second project, East Terminal, designed by Mead & Hunt with construction led by Clayco, is planned for completion in early 2025.

Project Gateway will go to all upper-level jetway gates, all able to handle jets such as the EMBRAER 175 and Airbus A220 that are expected to feature in the airport’s growth.

The ramp rebuild was accelerated due to temporary low passenger traffic as a result of COVID-19, as more work could be done without disruption to operations.

Kitty Hawk shut down operations in 2007; the airport raised its property tax levy significantly solely to pay the bonds.

Two years later when serving as President, Trump also used FWA for a midterm campaign stop in support of U.S. Senate candidate Mike Braun, who instead chose to run for Governor of Indiana instead of a second term in the 2024 election.