Paine Field was originally constructed in 1936 as a Works Progress Administration project. At the time of development, it was envisioned that the Airport would create jobs and economic growth in the region by becoming one of the ten new "super airports" around the country.

Paine Field was taken over by the U.S. Army Air Corps prior to entry into World War II as a patrol, air defense, and fighter training base and was later controlled by the U.S. Army Air Forces. With the end of the war, the airfield began to be returned to the civilian control of Snohomish County. In 1947, as transition activities were still underway, military control of the then-Paine Army Airfield was transferred to the newly established U.S. Air Force, with the facility renamed Paine Field. Transfer of the property to the Snohomish County government was completed in 1948, however, the Air Force continued to maintain various Air Defense Command units at the airport as military tenants.

Before Snohomish County could start planning for the continued development of a "super airport", the United States was again involved in an armed conflict—this time in Korea and also the breakout of the Cold War with the Soviet Union. When the Pacific Northwest defense installations were reviewed House Representative Henry M. Jackson recommended more military presence in the area and Paine Field was reactivated as a military airbase.

Paine Field was returned to USAF control in 1951, renamed Paine Air Force Base, and placed under the jurisdiction of the Air Defense Command (ADC). While the county relinquished most of its commercial facilities to house USAF personnel, units, and assets, the site did not have an exclusive military presence. The airfield remained a joint civil-military airport with the Air Force operating the control tower and other air traffic control facilities, while the county, in a shared-use agreement, rented commercial leasehold areas to businesses such as Alaska Airlines. The 4753rd Air Base Squadron (later re-designated the 86th Air Base Squadron) was activated on the new Air Force base on February 1, 1952, as a placeholder unit.

Although inactive for only six years, significant military construction (MILCON) was necessary to bring the World War II training base up to postwar USAF standards. In 1951, additional land surrounding the Paine AFB site was appropriated for military facilities and extended runways. A 9,000-foot jet runway (Rwy 16/34) was constructed along with accompanying taxiways, permanent concrete buildings, and other support facilities to replace the temporary wartime wooden structures that were viewed as substandard for a permanent USAF base. The 529th Air Defense Group was activated on February 16, 1953, and became the permanent host unit at Paine AFB until redesigned as the 326th Fighter Group in 1955.

Various regular Air Force fighter-interceptor units and Air Force Reserve troop carrier units operated at Paine AFB from 1951 until the mid-1960s. In 1966, USAF identified Paine AFB for closure due to budgetary constraints caused by the cost of the Vietnam War. The by then-host unit, the 57th Fighter Group phased down operations with the departure of the interceptors and was inactivated in place on September 30, 1968. Paine AFB has inactivated on the same date and the facility was returned to full civilian control as Paine Field / Snohomish County Airport. The 215th Engineering Installation Squadron (215 EIS) of the Washington Air National Guard, formerly situated at Paine Field, was inactivated in 2013.

Paine AFB / Paine Field had also been under consideration in the 1960s by Army Air Defense Command as one of several sites for the Sentinel Anti-Ballistic Missile System due to its central location to several other major military bases and defense industries in the Puget Sound Region. Sentinel was eventually dropped in favor of the limited Safeguard system.

On July 25, 1966, Boeing announced that it would build the Boeing 747, a jet airliner capable of carrying nearly twice as many passengers as previous models. To build the giant aircraft, Boeing had to construct a facility large enough to handle the world's largest commercial jetliner. The land just north of Paine Field was chosen to construct the new facilities, including some development on the airport itself. Both the local government and the FAA concurred with the development. Work on the massive building began in August 1966 and the first employees arrived in early 1967. The 747 made its first flight at Paine Field on February 9, 1969.

In 1984, the Snohomish County Council considered legislation to rename Paine Field for Senator Henry M. Jackson, who had died a few months earlier. The proposal was put on hold after the Port of Seattle renamed Seattle–Tacoma International Airport for Jackson, which sparked public outcry and force them to revert to the original name.

In late 2005, construction of the Future of Flight Aviation Center & Boeing Tour building was completed.