Project Run In completed operational tests in November 1954 and found the aircraft to be to USAF satisfaction and considerably better than the F-84G. However, ongoing engine failures resulted in the entire fleet being grounded in early 1955. Also, the J65 engine continued to suffer from flameouts when flying through heavy rain or snow. As the result of the problems, the active duty phaseout began almost as soon as the F-84F entered service in 1954, and was completed by 1958. Increased tensions in Germany associated with construction of the Berlin Wall in 1961 resulted in reactivation of the F-84F fleet. In 1962, the fleet was grounded due to the corrosion of control rods. A total of 1,800 man hours were expended to bring each aircraft to full operational capacity. Stress corrosion eventually forced the retirement of ANG F-84Fs in 1971.
On 9 March 1955, Lt. Col. Robert R. Scott, in a F-84F Thunderstreak, set a three-hour, 44-minute and 53-second record for the 2,446 mile flight from Los Angeles to New York.
With the appearance of the Republic F-105 Thunderchief, which also used wing-root mounted air intakes, the Thunderstreak became known as the Thud's Mother. The earlier F-84A had been nicknamed the "Hog" and the F-84F "Super Hog," the F-105 becoming the "Ultra Hog".
In what is probably one of the very few air-to-air engagements involving the F-84F, two Turkish Air Force F-84F Thunderstreaks shot down two Iraqi Il-28 Beagle bombers that crossed the Turkish border by mistake during a bombing operation against Iraqi Kurdish insurgents. This engagement took place on 16 August 1962.
The F-84F was retired from active service in 1964, and replaced by the North American F-100 Super Sabre. The RF-84F was replaced by the RF-101 Voodoo in USAF units, and relegated to duty in the Air National Guard. The last F-84F Thunderflash retired from the ANG in 1971. Three Hellenic Air Force RF-84Fs that were retired in 1991 were the last operational F-84s.