The F-100A officially entered USAF service on 27 September 1954 with 479th Fighter Wing at George AFB. By 10 November 1954, the F-100As suffered six major accidents due to flight instability, structural failures, and hydraulic system failures, prompting the Air Force to ground the entire fleet until February 1955. The 479th finally became operational in September 1955. Due to ongoing problems, the Air Force began phasing out the F-100A in 1958, with the last aircraft leaving active duty in 1961. By that time, 47 aircraft were lost in major accidents. Escalating tension due to construction of the Berlin Wall in August 1961 forced the USAF to recall the F-100As into active service in early 1962. The aircraft was finally retired in 1970.

The TAC request for a fighter-bomber was addressed with the F-100C which flew in March 1954 and entered service on 14 July 1955 with 450th Fighter Wing, Foster AFB. Operational testing in 1955 revealed that the F-100C was at best an interim solution, sharing all the vices of the F-100A. The uprated J57-P-21 engine boosted performance but continued to suffer from compressor stalls. On a positive note, the F-100C was considered an excellent platform for nuclear toss bombing because of its high top speed. The inertia coupling problem was more or less addressed with installation of a yaw damper in the 146th F-100C, later retrofitted to earlier aircraft. A pitch damper was added starting with the 301st F-100C, at a cost of US$10,000 per aircraft.

The addition of "wet" hardpoints meant the F-100C could carry a pair of 275 US gal (1,040 L) and a pair of 200 US gal (770 L) drop tanks. However, the combination caused loss of directional stability at high speeds and the four tanks were soon replaced by a pair of 450 US gal (1,730 L) drop tanks. The 450s proved scarce and expensive and were often replaced by smaller 335 US gal (1,290 L) tanks. Most troubling to TAC was the fact, that, as of 1965, only 125 F-100Cs were capable of utilizing all non-nuclear weapons in the Air Force inventory, particularly cluster bombs and AIM-9 Sidewinder air-to-air missiles.[1] By the time the F-100C was phased out in June 1970, 85 had been lost in major accidents.

The definitive F-100D aimed to address the offensive shortcomings of the F-100C by being primarily a ground attack aircraft with secondary fighter capability. To this effect, the aircraft was fitted with autopilot, upgraded avionics, and, starting with the 184th production aircraft, the Sidewinder capability. In 1959, 65 aircraft were modified to also fire the AGM-12 Bullpup air-to-ground missile. To further address the dangerous flight characteristics, the wing span was extended by 26 inches (66 cm) and the vertical tail area was increased by 27%.

The F-100D flew on 24 January 1956, entering service on 29 September 1956 with 405th Fighter Wing at Langley AFB. The aircraft suffered from reliability problems with the constant speed drive which provides constant-frequency current to electrical systems. In fact, the drive was so unreliable that USAF required it to have its own oil system to minimize damage in case of failure. Landing gear and brake parachute malfunctions claimed a number of aircraft, and the refueling probes had a tendency to break away during high speed maneuvers. Numerous post-production fixes created such a diversity of capabilities between individual aircraft that by 1965 around 700 F-100Ds underwent High Wire modifications to standardize the weapon systems. High Wire modifications took 60 days per aircraft at a total cost of US$150 million. In 1966, Combat Skyspot program fitted some F-100Ds with an X band radar transmitter to allow for ground-directed bombing in inclement weather or at night.

In 1967, the USAF began a structural reinforcement program to extend the aircraft's service life from the designed 3,000 flying hours to 7,000. Over 500 F-100Ds were lost, predominantly in accidents. After one aircraft suffered wing failure, particular attention was paid to lining the wings with external bracing strips. During the Vietnam War, combat losses constituted as many as 50 aircraft per year. On 7 June 1957, an F-100D fitted with an Astrodyne booster rocket making 150,000 lbf (667.2 kN) of thrust successfully performed a zero length launch. The capability was incorporated into late-production aircraft. After a major accident, the USAF Thunderbirds reverted from F-105 Thunderchief to the F-100D which they operated from 1964 until it was replaced by the F-4 Phantom II in 1968.

The F-100 was the subject of many modification programs over the course of its service. Many of these were improvements to electronics, structural strengthening, and projects to improve ease of maintenance. One of the more interesting of these was the replacement of the original afterburner of the J-57 engine with the more advanced afterburners from retired Convair F-102 Delta Dagger interceptors. This modification changed the appearance of the aft end of the F-100, doing away with the original "petal-style" exhaust. The afterburner modification started in the 1970s and solved maintenance problems with the old type as well as operational problems, including compressor stall problems.

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