The six-person flight crew consisted of Henry W. Hartsfield Jr., commander, making his second shuttle mission; pilot Michael L. Coats; three mission specialists – Judith A. Resnik, Richard M. Mullane and Steven A. Hawley; and a payload specialist, Charles D. Walker, an employee of McDonnell Douglas. Walker was the first commercially sponsored payload specialist to fly aboard the Space Shuttle. Resnik became the second American woman to fly any NASA space mission, after Sally K. Ride.

Primary cargo of Discovery consisted of three commercial communications satellites: SBS-D for Satellite Business Systems, Telstar 302 for Telesat of Canada, and Syncom IV-2, or Leasat-2, a Hughes-built satellite leased to the US Navy. Leasat-2 was the first large communications satellite designed specifically to be deployed from the Space Shuttle. All three satellites were deployed successfully and became operational.

Another payload was the OAST-1 solar array, a device 13 feet (4.0 m) wide and 102 feet (31 m) high, which folded into a package 7 inches (180 mm) deep. The array carried a number of different types of experimental solar cells and was extended to its full height several times during the mission. At the time, it was the largest structure ever extended from a crewed spacecraft, and it demonstrated the feasibility of large lightweight solar arrays for use on future orbital installations, such as the International Space Station.

The McDonnell Douglas-sponsored Continuous Flow Electrophoresis System (CFES) experiment, using living cells, was more elaborate than the one flown on previous missions, and payload specialist Walker operated it for more than 100 hours during the flight. A student experiment to study crystal growth in microgravity was also carried out. The highlights of the mission were filmed using an IMAX motion picture camera, and later appeared in the 1985 documentary film The Dream is Alive. Because of an obstruction in the shuttle's external wastewater dumping system, a two-foot "pee-sicle" formed during the mission; Hartsfield removed it with the Remote Manipulator System.

On 3 September, concern arose over the formation of ice on the waste dump nozzle of the shuttle. The next day, Hartsfield used the shuttle’s robotic arm to dislodge the large chunk of ice.

The mission lasted 6 days, 00 hours, 56 minutes, 04 seconds, with landing taking place on Runway 17 at Edwards Air Force Base at 6:37 a.m. PDT on 5 September 1984. During STS-41-D, Discovery traveled a total of 2,490,000 miles (4,010,000 km) and made 97 orbits. The orbiter was transported back to KSC on 10 September 1984. Ominously, STS-41-D was the first Shuttle mission in which blow-by damage to the SRB O-rings was discovered, with a small amount of soot found beyond the primary O-ring. Following the Challenger tragedy, Morton Thiokol engineer Brian Russell called this finding the first "big red flag" on SRB Joint and O-ring safety.