Atlantis launched from Kennedy Space Center on November 15, 1990 at 6:48 PM EST and landed at Kennedy on November 20 at 4:42 PM EST. The shuttle orbited 79 times at an altitude of 142 nautical miles at an inclination of 28.5 degrees and travelled 2 million miles.

This was a Department of Defense mission and the mission activities are classified.

The launch was originally scheduled for July 1990. However, a liquid hydrogen leak found on the orbiter Columbia during the STS-35 countdown prompted three precautionary tanking tests on Atlantis at the pad on June 29, July 13 and July 25. Tests confirmed a hydrogen fuel leak on external tank side of external tank/orbiter 17-inch quick disconnect umbilical. This could not be repaired at the pad and Atlantis rolled back to the VAB on August 9, was demated and transferred to the OPF.

During rollback, the vehicle parked outside the VAB about a day while COLUMBIA/STS-35 stack was transferred to the pad for launch. Outside, Atlantis suffered minor hail damage to tiles during a thunderstorm. After repairs were made in the OPF, Atlantis was transferred to the VAB for mating on October 2. During hoisting operations, a platform beam that should have been removed from aft compartment fell and caused minor damage which was repaired. Vehicle rolled out to Pad A on October 12. Fourth mini-tanking test performed October 24, with no excessive hydrogen or oxygen leakage detected.

At Flight Readiness Review, launch date was set for November 9. Launch was reset for November 15 due to payload problems. Liftoff occurred during a classified launch window lying within a launch period extending from 6:30 to 10:30 p.m. EST, November 15, 1990.

Atlantis was crewed by Commander Richard O. Covey, Pilot Frank L. Culbertson, and Mission Specialists Robert C. Springer, Carl J. Meade, And Charles D. Gemar.