Prior to the construction of this airport, the Toowoomba region had not been serviced by a jet-capable airport at any time in the city's history. The existing Toowoomba City Aerodrome at Wilsonton in suburban residential Toowoomba has been historically restricted in development due to local council land development policy and poor local planning, although a runway extension in 2011 allowed for improved scheduled services with turboprop aircraft.

The Darling Downs and Surat Basin regions were subject to significant growth between 2005 and 2013, primarily due to coal mining and coal seam gas exploration. This industrial expansion coupled with the development of a transport hub and industrial estate at Charlton (10 km west of Toowoomba) provided the land corridor immediately west of Toowoomba with government-endorsed transport development opportunities.

Construction on the site, a former quarry owned by the Wagner family since 1994, began in April 2013, with an ambitious timeframe for completion by October 2014.

On 22 November 2013, a Beechcraft King Air owned and piloted by John Wagner became the first aircraft to land on the new runway. On 15 January 2014, the first concrete for the terminal building was poured. In June 2014, work began on sealing the runway and movement areas using EFC, a low-carbon cement-free concrete developed by Wagners, boosting the airport's green credentials.

On 3 September 2014, Qantas became the first airline to announce regular services from the airport. Regional services operated under contract to the Government of Queensland transferred from Toowoomba City Aerodrome to Wellcamp on 1 January 2015. On 17 November 2014, the first scheduled passenger service commenced, operating between Sydney Airport and Wellcamp airport.

On 23 November 2015, the first jumbo aircraft arrived from Sydney. The Cathay Pacific 747 freighter aircraft made a brief stop en route from Sydney Airport to Hong Kong to collect produce bound for China. The trial service uplifted 58 tonnes of fresh produce during the stop.

In March 2016, services to Cairns and Melbourne with Airnorth commenced, followed by Townsville in November.

In October 2016, Cathay Pacific announced the opening of weekly cargo services starting on 22 November 2016, from Wellcamp to Hong Kong using a 747 freighter aircraft. This service operated from Hong Kong to Sydney, and returning via stops in Melbourne and Wellcamp. Cathay Pacific also announced that the first cargo export booking from Toowoomba was for a live crocodile.

On 22 October 2016, the first international passenger flight stopped at Wellcamp airport. This also marked the first Airbus A330 flight at the airport. The service was a charter originating in Sydney before stopping at Wellcamp to collect 250 people traveling to Shanghai, China for a trade conference.

On 11 November 2016, the airport was designated as an international airport and as a regional international gateway.

In July 2018, Airnorth announced the cancellation of the Wellcamp-Cairns route from October 2018.

In 2019, a one off flight to the airport was carried out by TNT, as well as DHL later that year.

In September 2022, Virgin Orbit signed an agreement with Wagners to base a Boeing 747-400 launch aircraft at the airport with a demonstrator small satellite launch initially planned for 2024. However, in April 2023, Virgin Orbit filed for bankruptcy, with no launches ever taking place.

In May 2025, Cathay Pacific announced that the last scheduled cargo flight would be on 10 June 2025. From there, the service would be moved to Brisbane Airport, first flying on 17 June 2025.