In 2293, the Challenger was assigned a deep space exploration mission. The ship was named on a Starship Mission Assignments chart on the USS Enterprise-A bridge. (Star Trek VI: The Undiscovered Country)
According to a ship list included in the plans, and not seen in the extended cut of the movie, the Challenger was commanded by M. Michaels, and the ship was located in Sector 21166. The captain was named after the sixth movie's set decorator Mickey S. Michaels. 
In the non-canon board game Star Fleet Battles, USS Challenger was a Byrd-class Galactic Survey Cruiser, a modification of the Constitution-class which replaces the photon torpedoes with special scientific sensor equipment.