In the late 1950s the USAF sought a replacement for its F-106 Delta Dart interceptor. As part of the Long Range Interceptor Experimental (LRI,X) program, the North American XF-108 Rapier, an interceptor with Mach 3 speed, was selected. However, the F-108 program was canceled by the Department of Defense in September 1959. During this time Lockheed's Skunk Works was developing the A-12 reconnaisance aircraft for the CIA under the Oxcart program. Kelly Johnson, the head of Skunk Works, proposed to build a version of the A-12 named AF-12 by the company; the USAF ordered three AF-12s in mid-1960.

The AF-12s took the seventh through ninth slots on the A-12 assembly line; these were designated as YF-12A interceptors. The main changes involved modifying the A-12's nose to accommodate the Hughes AN/ASG-18 fire-control radar originally developed for the XF-108, and the addition of the second cockpit for a crew member to operate the fire control radar for the air-to-air missle system. The modifications changed the aircraft's aerodynamics enough to require ventral fins to be mounted under the fuselage and engine nacelles to maintain stability. The four bays previously used to house the A-12's reconnaissance equipment were converted to carry Hughes AIM 47 Falcon (GAR-9) missiles. One bay was used for fire control equipment.

The first YF-12A flew on 7 August 1963. President Lyndon B.Johnson announced the existence of the aircraft on 24 February 1964. The YF-12A was announced in part to continue hiding the A-12, its still-secret ancestor; any sightings of CIA/Air Force A-12s based at Area 51 in Nevada could be attributed to the well-publicized Air Force YF-12As based at Edwards AFB in California.

On 14 May 1965 the Air Force placed a production order for 93 F-12Bs for its air Defense Command (ADC). However, Secretary of Defense Robert McNamara would not release the funding for three consecutive years due to Vietnam war costs. Updated intelligence placed a lower priority on defense of the continental US, so the F-12B was deemed no longer needed. Then in January 1968, the F-12B program was officially ended

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