What is today Cannon AFB began as a very small civilian passenger air field in the 1920s, Portair Field. It was renamed in the 1930s to Clovis Air Field, after the nearby town of Clovis.

With the arrival of World War Two, Clovis Air Field was acquired by the US Army and assigned to the Second Air Force, and renamed Clovis Army Air Base. The main mission of Clovis AAF was training bomber crews for several groups of the 16th Bombardment Wing. At the end of the war, Clovis was assigned to Strategic Air Command for ongoing bomber training, then inactivated in 1947 due to post-war budget cuts.

Clovis was reactivated less than six months later, with the separation of the Army and Air Force, and placed on reserve for three years, followed by a full activation as a tactical fighter base for the Korean War. Clovis housed the 140th Fighter-Bomber Wing, composed of Air National Guard units from around the country, which served in Korea and Operation Snapper-Tumbler, an early nuclear bomb test in Nevada.

Clovis was renamed Cannon Air Force Base in 1957, in honor of General John K. Cannon, a former commander of the Tactical Air Wing.

Other units assigned to Clovis / Cannon AFB included the 50th Fighter-Bomber Wing, 388th Fighter-Bomber Wing, the 312th/474th Fighter-Bomber Wings, and the 27th Tactical Fighter Wing. Squadrons of the 27th were assigned to missions related to the Berlin Crisis of 1961 and the Cuban Missile Crisis, and deployed to Vietnam throughout the 1960s and into the 1970s.

After the Cold War, squadrons from Cannon were assigned to Operations Desert Shield and Desert Storm, and with the reorganizations of the 1990s and 2000s, squadrons from Cannona have been deployed around the world on many missions. In the 2000s the 27th Fighter Wing was reorganized and redesignated the 27th Special Operations Wing, and Cannon AFB has reorganized its base role.