During the program's early years, from 1984 to mid-1992, the F-117A fleet was based at Tonopah Test Range Airport, Nevada where it served under the 4450th Tactical Group. Because the F-117 was classified during this time, the unit was officially located at Nellis Air Force Base, Nevada and equipped with A-7 Corsair II aircraft. All military personnel were permanently assigned to Nellis AFB, but most personnel and their families lived in the Las Vegas. This required commercial air and trucking to transport personnel between Las Vegas and Tonopah each week. The 4450th was absorbed by the 37th Tactical Fighter Wing in 1989. In 1992, the entire fleet was transferred to Holloman Air Force Base, New Mexico, where it was placed under the command of the 49th Fighter Wing. This move also eliminated the Key Air and American Trans Air contract flights to Tonopah, which flew 22,000 passenger trips on 300 flights from Nellis to Tonopah per month.
F-117 pilots called themselves "Bandits". Each of the 558 Air Force pilots who have flown the F-117 have a Bandit number, such as "Bandit 52", that indicates the sequential order of their first flight in the F-117.
The F-117 has been used several times in war. Its first mission was during the United States invasion of Panama in 1989. During that invasion two F-117A Nighthawks dropped two bombs on Rio Hato airfield.
During the Gulf War in 1991, the F-117A flew approximately 1,300 sorties and scored direct hits on 1,600 high-value targets in Iraq over 6,905 flight hours. Leaflet drops on Iraqi forces displayed the F-117 destroying ground targets and warned "Escape now and save yourselves". Initial claims of its effectiveness were later found to be overstated. For instance it was claimed that the F-117 made up 2.5% of Coalition tactical aircraft in Iraq and they attacked more than 40% of the strategic targets; this ignored the fact that only 229 Coalition aircraft could drop and designate laser-guided bombs of which 36 F-117 represented 15.7%, and only the USAF had the I-2000 bombs intended for hardened targets, so the F-117 represented 32% of all coalition aircraft that could deliver such bombs. Initial reports of them hitting 80% of their targets were later scaled back to "41-60%". On the first night they failed to hit 40% of the air-defense targets they were assigned, including the Air Defense Operations Center in Baghdad, and 8 such targets remained functional out of 10 that could be assessed. In their Desert Storm white paper the USAF claimed that "the F-117 was the only airplane that the planners dared risk over downtown Baghdad" and that this area was particularly well defended. In fact most of the air defenses were on the outskirts of the city and many other aircraft hit targets in the downtown area, with minimal casualties when they attacked at night like the F-117. This meant they avoided the optically aimed AAA and infra-red SAMs which were the biggest threat to Coalition aircraft.
The aircraft was operated in secret from Tonopah for almost a decade, but after the Gulf War the aircraft moved to Holloman in 1992. Its integration with the USAF's non-stealth "iron jets" occurred slowly, however; because of ongoing secrecy, others continued to see the aircraft, as one senior F-117A pilot later said, "none of their business, a stand-alone system". The F-117A and the men and women of the 49th Fighter Wing were deployed to Southwest Asia on multiple occasions. On their first deployment, with the aid of aerial refueling, pilots flew non-stop from Holloman to Kuwait, a flight of approximately 18.5 hours – a record for single-seat fighters that stands today.