Lunar Prospector was a spacecraft that orbited the Moon for 19 months in 1998-99. From a low polar orbit, it mapped surface composition including lunar hydrogen deposits, measured magnetic and gravity fields, and studied lunar outgassing events. The mission ended July 31, 1999, when the orbiter was deliberately crashed into a crater near the lunar south pole.

Data from the mission provided detailed mapping of the surface composition of the Moon, and helped to improve understanding of the origin, evolution, current state, and resources of the Moon. The mission identified the presence of hydrogen, implying deposits of ice on the Moon. Several articles on the scientific results were published in the journal Science.

Lunar Prospector was the third mission selected by NASA for full development and construction as part of the Discovery Program. It was managed by NASA Ames Research Center with the prime contractor being Lockheed Martin; it cost $62.8 million. The Principal Investigator for the mission was Alan Binder. His personal account of the mission, Lunar Prospector: Against all Odds, is highly critical of the bureaucracy of NASA overall, and of its contractors.

The spacecraft was a graphite-epoxy drum, 1.36 m (4 ft 6 in) in diameter and 1.28 m (4 ft 2 in) high with three radial 2.5 m (8 ft 2 in) instrument booms. A 1.1 m (3 ft 7 in) extension boom at the end of one of the 2.5 m booms held the magnetometer. Total initial mass (fully fueled) was 296 kg (653 lb). It was spin-stabilized (nominal spin rate 12 rpm) with its spin axis normal to the ecliptic plane. The spacecraft was controlled by six hydrazine monopropellant 22-newton thrusters (two aft, two forward, and two tangential). Three fuel tanks mounted inside the drum held 138 kg (304 lb) of hydrazine pressurized by helium. The power system consisted of body-mounted solar cells which produced an average of 186 W and a 4.8 A·h rechargeable NiCd battery.

Communications were through two S band transponders, a slotted, phased-array medium-gain antenna for downlink, and an omnidirectional low-gain antenna for downlink and uplink. The on-board computer was a Harris 80C86 (based on Intel's 8086) with 64 kilobytes of EEPROM and 64 kilobytes of static RAM. All control was from the ground, the computer echoing each command to the ground for verification there. Once the command was ground-verified, an "execute" command from the ground told the computer to proceed with execution of the command. The computer built telemetry data as a combination of immediate data and also read from a circular queue buffer which allowed the computer to repeat data it had read 53 minutes earlier. This simple solid-state recorder ensured that all data collected during communications blackout periods would be received, providing the blackout was not longer than 53 minutes.

The probe also carried a small amount of the remains of Eugene Shoemaker (April 28, 1928 – July 18, 1997), astrogeologist and co-discoverer of Comet Shoemaker-Levy 9, to the Moon for a space burial.

In 2013 an unidentified piece of space junk was discovered in an unstable orbit around the Earth, and assigned the provisional number WT1190F. After it crashed into the Indian Ocean, the object was identified as probably the translunar injector of Lunar Prospector.

Following launch on January 7, 1998 UT (January 6 EST) aboard a four-stage Athena II rocket, Lunar Prospector had a 105-hour cruise to the Moon. During the cruise, the three instrument booms were deployed. The MAG and APS collected calibration data, while the GRS, NS, and ER outgassed for one day, after which they also collected calibration data in cislunar space. The craft was inserted into an 11.6-hour period capture orbit about the Moon at the end of the cruise phase. After 24 hours Lunar Prospector was inserted into a 3.5-hour period intermediate orbit, followed 24 hours later (on January 13, 1998) by transfer into a 92 km × 153 km (57 mi × 95 mi) preliminary mapping orbit, and then on January 16 by insertion into the near-circular 100 km (62 mi) altitude nominal lunar polar mapping orbit with an inclination of 90 degrees and a period of 118 minutes. Lunar calibration data was collected during the 11.6- and 3.5-hour orbits. Lunar mapping data collection started shortly after the 118 minute orbit was achieved. The data collection was periodically interrupted during the mission as planned for orbital maintenance burns, which took place to recircularize the orbit whenever the periselene or aposelene was more than 20 km (12 mi) to 25 km (16 mi) from the 100 km nominal orbit; this occurred about once per month. On December 19, 1998, a maneuver lowered the orbit to 40 km (25 mi) to perform higher resolution studies. The orbit was altered again on January 28 to a 15 km × 45 km (9.3 mi × 28.0 mi) orbit, ending the one year primary mission and beginning the extended mission.