The Lunar Prospector was designed for a low polar orbit investigation of the Moon, including mapping of surface composition and possible polar ice deposits, measurements of magnetic and gravity fields, and study of lunar outgassing events. Data from the 1 to 3 year mission will allow construction of a detailed map of the surface composition of the Moon, and will improve understanding of the origin, evolution, current state, and resources of the Moon. After launch, the Lunar Prospector had a 105 hour cruise to the Moon, followed by insertion into a near-circular 100 km altitude lunar polar orbit with a period of 118 minutes. The nominal mission duration was one year.

A two year extended mission following the original one-year mission was possible, during which the orbit was to be lowered to 50 km and then 10 km altitude to obtain higher resolution measurements. However this was not funded, and the spacecraft was commanded to crash into the moon.