The airport was previously named Waterloo Regional Airport, but it changed its name in March 2004 after Northwest Airlines announced that it would run daily flights to Detroit, Michigan.

Construction began on the Kitchener-Waterloo Municipal Airport, also known as Lexington Airport, in 1929, on the Heinrich farm on Lexington Road in Waterloo. The towns of Kitchener and Waterloo and the Ontario Equitable Life and Accident Insurance Company acquired the lands to build a land and water airport facility. Completed in 1930, the airfield was mainly used for flying instruction. The airport had two grass runways (1,800 ft [550 m] and 2,000 ft [610 m]) on 83 acres (34 ha) on the southeast side of Lexington Road.

Gilles Air Service began to operate from the airfield from 1930 to 1932 and was succeeded by Kitchener-Waterloo Flying Club from 1932 to 1951. During World War II, civilian aviation ceased at the airfield and it was used by the British Commonwealth Air Training Plan.

At the end of the war, there was a push for a larger and more appropriate place for private and commercial aviation in the area. In 1948, the Waterloo-Wellington Airport Commission acquired a larger site in the Breslau, Ontario, area and a new airfield opened there in 1950.

The original airport was sold in 1951 to A.B. Caya and re-developed into a mixed residential and commercial area. The entrance to the former airport is now Lexington Park at 291 Lexington Road.

The new K-W Municipal Airport became a general aviation facility in 1969. From 1951 to 1973, the Waterloo-Wellington Flying Club ran the airport and then sold it to Waterloo Region and the City of Guelph. It became a publicly owned airport and was renamed Waterloo Regional Airport. Today it operates 24 hours, seven days a week.

The airport's former name, Waterloo Regional Airport, is now used by Waterloo Regional Airport in Waterloo, Iowa.

In November 2020, Waterloo was the busiest airport in Canada, owing to the continued operation of its flight-training businesses while much of Canadian aviation was shut down by the COVID-19 pandemic in Ontario.

Lexington Airport then and now

A historical plaque near the entrance of Lexington Park describes the runways.

Expansion

Waterloo underwent a major expansion in 2003. Starting in 2008, the airport started expanding again to accommodate larger aircraft on the aprons and taxiways; this includes widening the main apron 3, expanding apron 2 into apron 3, new widened taxiway alpha and Charlie taxiway off apron 2 to runway 08, and approach lighting on runway 26. In 2010, Taxiway Charlie was widened to prepare for a new development area called "LL4." A new general manager recruited from the Greater Toronto Airports Authority, Chris Wood, was appointed in September 2009.

Northwest Airlines affiliate Mesaba Airlines flew to Detroit until June 2009.

In late 2005, major vacation charters (primarily to the Caribbean) began to operate during their peak season, notably Sunwing Airlines to Cancún.

WestJet launched daily flights to Calgary on 14 May 2007. This was initially labelled a seasonal service, but on 27 June 2007, WestJet announced that the flights would continue year-round. WestJet also operated daily seasonal flights to Vancouver in the summer of 2010, but these did not continue in subsequent years.

Bearskin Airlines started daily non-stop flights to Ottawa on 1 October 2007, with onward connections to Northern Ontario, and added daily flights to Montreal beginning on 1 May 2011. The Montreal flights ended in September 2012, and on 25 March 2014, Bearskin announced that they would terminate all scheduled service from the airport effective 1 April 2014. They continued to operate charter flights at the airport.

On 13 December 2011, American Airlines announced new daily nonstop flights to Chicago beginning on 14 June 2012, the airport's first destination in the United States since 2009. The service was operated by Envoy under the American Eagle brand, using Embraer 145 jets. On 22 June 2016, American Airlines announced they would be suspending flights effective 5 October 2016.

In September 2013, Nolinor Aviation began three weekly and four every other week charter service from the airport to Mary River via Iqaluit with a Boeing 737-200 combi. This service was expected to bring $400,000 annually to the airport through landing and ramp fees with no additional costs to the region. Nolinor no longer makes regular flights out of the airport.

A new air traffic control tower commenced operations on 27 September 2017, replacing the original tower built in 1969. This tower is an additional 16 feet taller (80 feet) and 85 square feet bigger than the previous tower.

Low-cost carrier Flair Airlines began flying to six domestic destinations in May 2021. This was later expanded to 9 Canadian destinations plus 2 US and Cancún, Mexico - some of them seasonal.

In April 2021, Waterloo Regional Council approved $44 million to further the expansion of the airport. As part of this expansion, the airport will get increased baggage handling capacity and larger departure lounges. This was completed in 2023.