The history of RAF Molesworth dates back to 1917 when it was selected by the Royal Flying Corps as a site for an airfield. The first flying unit to use Molesworth was the 75th Squadron. After World War I ended, the airfield was abandoned. During World War II, the airfield was used by the US 15th Bombardment Squadron, which arrived on 9 June 1942, and used the Douglas Boston III (A-20) light bomber. It was later the home of the 303rd Bombardment Group, which flew the B-17G “Flying Fortress.” The 303rd would remain at Molesworth until shortly after V-E Day in late May 1945. The group would become one of the legendary units of the Eighth Air Force. The 303rd received a Distinguished Unit Citation for an operation on 11 January 1944 and in total flew 364 missions comprising 10,271 sorties. The group saw 817 of its men killed in action with another 754 becoming prisoners of war. On 31 May 1945, the 303rd Bomb Group left Molesworth, moving to Casablanca, French Morocco. On 1 July 1945 the Americans turned the station back to the RAF, who quickly chose it to be a training base for their new jet aircraft. The first jet unit, 1335th Conversion Unit, arrived on 27 July, flying Gloster Meteor IIIs.
In 1973 the airfield was officially deactivated. The only remaining structures on the station were a small arms firing range, used by USAF personnel for target practice, a compound for surplus and obsolete USAF vehicles, a derelict watchtower and a warehouse.
In June 1980, RAF Molesworth was selected as one of two British bases for the US Air Force's mobile nuclear armed Ground Launched Cruise Missiles or GLCMs. On 12 December 1986 the 303rd Tactical Missile Wing was activated. However, the missiles and the wing did not stay long; the United States and the Soviet Union signed the Intermediate-Range Nuclear Forces Treaty in 1987 which led to the removal of all nuclear missiles from the station by October 1988. The 303rd Tactical Missile Wing was inactivated on 30 January 1989.
On 11 January 1990 the RAF announced construction would begin to house the U.S. European Command's new intelligence analysis centre. This facility would become known as the Joint Analysis Center (JAC), now the Joint Intelligence Operations Center Europe (JIOCEUR) Analytic Center. The unit has provided intelligence support for US and NATO missions in the Middle East, the Balkans and in support of counter-terrorist operations since 11 September 2001.