During launch the Challenger experienced multiple sensor failings in its SSMEs and had to perform an "Abort to Orbit" (ATO) emergency procedure. It is the only mission to have carried out an abort of any kind. As a result of the ATO, the mission was carried out at a slightly lower orbital altitude.

STS-51-F's primary payload was the laboratory module Spacelab 2. A special part of the modular Spacelab system, the "igloo", which was located at head of a three-pallet train, provided on-site support to instruments mounted on pallets. The main mission objective was to verify performance of Spacelab systems, determine the interface capability of the orbiter, and measure the environment created by the spacecraft. Experiments covered life sciences, plasma physics, astronomy, high-energy astrophysics, solar physics, atmospheric physics and technology research. Despite mission replanning necessitated by Challenger's abort to orbit trajectory, the Spacelab mission was declared a success.

The flight marked the first time the ESA Instrument Pointing System (IPS) was tested in orbit. This unique pointing instrument was designed with an accuracy of one arcsecond. Initially, some problems were experienced when it was commanded to track the Sun, but a series of software fixes were made and the problem was corrected. In addition, Tony England became the second amateur radio operator to transmit from space during the mission.

The Spacelab Infrared Telescope (IRT) was also flown on the mission.The IRT was a 15.2 cm aperture helium-cooled infrared telescope, observing light between wavelengths of 1.7 to 118 μm. The experiment experienced some problems, such as heat emissions from the Shuttle corrupting data, but still returned useful astronomical data.

The Plasma Diagnostics Package (PDP), which had been previously flown on STS-3, made its return on the mission, and was part of a set of plasma physics experiments designed to study the Earth's ionosphere. During the third day of the mission, it was grappled out of the payload bay by the Remote Manipulator System and released for six hours. During this time, Challenger maneuvered around the PDP as part of a proximity operations exercise. The PDP was successfully grappled by the RMS and returned to the payload bay at the beginning of the fourth day of the mission.

In a heavily-publicized marketing experiment, astronauts aboard STS-51-F drank carbonated beverages from specially-designed cans provided by competitors Coca-Cola and Pepsi.Post-flight, the astronauts revealed that they preferred Tang, in part because it could be mixed on-orbit with existing chilled water supplies, whereas there was no dedicated refrigeration equipment on board to chill the soda, which also fizzed excessively in microgravity