Launch from Cape Canaveral (KSC) and landing on Cape Canaveral (KSC), Runway 33.

Launch was originally scheduled for July 1990. However, a liquid hydrogen leak found on orbiter Columbia during STS-35 countdown prompted three precautionary tanking tests on Atlantis at pad June 29, 1990, July 13, 1990 and July 25, 1990. Tests confirmed the hydrogen fuel leak on the external tank side of the external tank/orbiter 432 millimeters (17.0 in) quick disconnect umbilical. This could not be repaired at the pad and Atlantis rolled back to the VAB on August 09, 1990, was demated, then transferred to the Orbiter Processing Facility (OPF). During rollback, the vehicle remained parked outside the VAB for about a day while the Columbia/STS-35 stack was transferred to the pad for launch. While outside, Atlantis suffered minor hail damage to its tiles during a thunderstorm. After repairs were made in the OPF, Atlantis was transferred to the VAB for mating on October 02, 1990. During hoisting operations, the platform beam that should have been removed from aft compartment fell and caused minor damage, which was repaired. The vehicle rolled out to Pad A on October 12, 1990. The fourth mini-tanking test was performed on October 24, 1990, with no excessive hydrogen or oxygen leakage detected. During the Flight Readiness Review, the launch date was set for November 09, 1990. Launch was reset for November 15, 1990 due to payload problems.

This flight was the seventh mission dedicated to the Department of Defense, and most information about it remained classified. For another time, NASA did not provide pre-launch commentary to the public until nine minutes before liftoff. It was the fifth military mission without a MSE among the crew members.

Main goal was the deployment of the reconnaissance satellite AFP-658 (Magnum-3; USA-67. According to Aviation Week, this satellite was gathering satellite headed for geosynchronous orbit like those launched by STS-51C and STS-33, launched to monitor the events during the first Gulf War in 1990. Also, according to Aviation Week, the shuttle initially entered a 204 kilometers (127 mi) x 519 kilometers (322 mi) orbit at an inclination of 28.45° to the equator. It then executed three OMS (orbital maneuvering system) burns, the last on orbit #4. The first of these circularized the orbit at 519 kilometers (322 mi). Later observers have speculated that USA-67 was instead a secret SDS-2 military communications satellite, like those deployed on STS-28 and STS-53. A publicly released image of the vertical stabilizer and upper aft bulkhead, similar to the one released from STS-53, confirms that the ASE (Airborne Support Equipment) for the IUS was absent from this flight. The satellite was deployed on the 7^th orbit and then ignited its rocket motor at the ascending node of the 8^th orbit, to place it in a geo-synchronous transfer orbit. Rumors that now appear to have been substantiated by the identification of an "unknown" geostationary satellite by amateur observers insist that a second secret payload was deployed: Prowler. Prowler is reportedly a stealth satellite intended to covertly inspect other nation's geostationary satellites

The mission was extended one day, because of too high crosswinds at the original planned landing site Edwards AFB. Continued adverse conditions led to decision to shift landing to KSC.