Shortly after World War II was declared, the Government of Newfoundland turned the operation of the airfield over to the Royal Canadian Air Force (RCAF) in 1940, which had been tasked by the United Kingdom the responsibility to provide aerial defense for the dominion.

10 Bomber and Reconnaissance (BR) Squadron began operating from the airfield, flying Douglas Digbys and later, Liberators with responsibility to protect supply convoys in the North Atlantic from enemy U-boats.

The airfield was renamed RCAF Station Gander in 1941 and it became heavily used by Ferry Command for transporting military aircraft from Canada and the United States to the European theatre.

When Newfoundland joined Confederation, the RCN formally acquired the property known as the "Old Navy Site" and Naval Radio station Gander, call sign CGV, was born.

As a GCI station, the squadron's role was to guide interceptor aircraft toward unidentified intruders picked up on the unit's radar scopes.

In 1977, Gander saw its first military flying unit return to the area since the war when a detachment of 424 Squadron, flying CH-113 Labrador helicopters moved to CFS Gander to provide search and rescue (SAR) operations (this being in response to Canada declaring its 200-nautical-mile (370 km) Exclusive Economic Zone offshore, resulting in increased Canadian fishing activities).

Having found a permanent home at Gander, the SAR helicopters were no longer a 424 Squadron detachment and a new unit identifier was required.

During the early 1990s the federal government began to cut back on its defence budget, resulting in numerous base closures across Canada.

Among its many roles, 9 Wing Gander is responsible for providing search and rescue services throughout Newfoundland and Labrador, northeastern Quebec, the eastern Arctic and offshore waters of these regions.

CFB Gander is also host to the Leitrim Detachment which operates and maintains signals intelligence and utilizes a Wullenweber AN/FRD-10 circularly disposed antenna array for High-frequency direction finding of high-priority targets.

9 Wing Telecommunications provides all military air units at Gander with message transmission and reception services.