The airport started in 1939 as a grass strip, and was used as a military training airfield. During the early part of World War II (1940–1941), the airfield was used as Royal Air Force Station Patricia Bay, providing basic flight training for Royal Air Force pilots preparatory to returning them to the UK.

In approximately 1942 the aerodrome became a Royal Canadian Air Force (RCAF) installation listed as RCAF Aerodrome - Patricia Bay, British Columbia at 48°39′N 123°26′W with a variation of 24 degrees east and elevation of 25 ft (7.6 m). The aerodrome was listed with three runways as follows:

The airport is located beside Patricia Bay, which, due to the prevalence of flying boats at the time, proved to be an excellent location. The Department of Transport took over the airport in 1948. It was then called Victoria (Patricia Bay) Airport, and many locals still refer to it as the "Pat Bay Airport". Trans-Canada Airlines (later Air Canada) began regular service in 1943.

In 1959, the airport was renamed the "Victoria International Airport".

The last RCAF unit left the airport in 1952. In July 1989, Canadian Forces Air Command returned to Victoria International Airport when HS 443 Squadron, which operated CH-124 Sea King ship-borne anti-submarine warfare (ASW) helicopters, was relocated from CFB Shearwater to better support Canadian Forces Maritime Command operations in the Pacific. In 1995, the squadron was redesignated as 443 Maritime Helicopter Squadron.

In 1997, as part of a broad scale restructuring of airports across Canada, Transport Canada (formerly the Department of Transport), gave operational control of the airport to the Victoria Airport Authority.

In 2000, the Victoria Airport Authority began the process of renovating and expanding the terminal to meet passenger needs. In 2002, the new airside hold room and the new arrivals rotunda were rebuilt. By 2005, the new departures area was completed.

In May 2005, the federal government, which owns the land, announced a reduction in the rent paid by the Victoria Airport Authority. This will save $0.6 million each year and $12 million over the life of the lease, which is 50 years.

In 2015, 443 Maritime Helicopter Squadron moved into a new $155 million heliport at the airport, which the RCAF titled Arundel Castle after the major landmark of that name in West Sussex, the English county where the unit operated when it was a fighter squadron flying the Supermarine Spitfire during World War II. The main mission of 443 Squadron in the 21st century is to provide ASW and logistical support for the Royal Canadian Navy. As of 2022, 443 Squadron is responsible for all Canadian west coast operations of the CH-148 Cyclone helicopter.

In July 2016, WestJet announced that they would be permanently ending service to Honolulu from Victoria. The non-stop route had started in 2009 and had ended due to the lack of demand.

In September 2018, United Airlines announced that the daily United Express flight from Victoria to San Francisco would permanently end on January 7, 2019, concluding over a decade of daily non-stop service between the two cities.

In March 2019, Delta Air Lines announced that all Delta flights from Victoria to Seattle would permanently end on September 2, 2019, concluding a three-year presence by the airline in Victoria and leaving Alaska Airlines as the only airline serving Victoria directly from Seattle or anywhere in the United States. Delta was the second airline to leave Victoria that year, after United Airlines withdrew service in January 2019.