The follow-up mission of Clementine occurred 4 years later, when on January 6, 1998 NASA launched the Lunar Prospector spacecraft.

The objectives of Lunar Prospector, which was designed to achieve reliability and low cost, was to collect data from the moon that had to do with the chemical composition of its surface, the location of lunar energy sources, its magnetic and gravitation field and finally to study lunar out gassing events (TLP). For this purpose the spacecraft carried only scientific instruments and no cameras. In this way, the data collected from previous missions could be completed, giving us a better understanding of the origin, the evolution and the current state of the moon.

In the main part of the mission, Lunar Prospector, by using its instruments (Gamma Ray Spectrometer, Neutron Spectrometer, Alpha Particle Spectrometer, Magnetometer, Electron Reflectometer), spent one year mapping the entire surface of the Moon from a distance of about 100 kilometers. After achieving its primary targets, the mission was extended for an additional seven months. At this time, the orbit of the spacecraft was lowered, first to about 30 kilometers and then to within about 10 kilometers of the lunar surface, allowing the spacecraft to obtain data at much higher resolutions.

Among the early returns from the instruments were those from the Neutron Spectrometer, indicating significant amounts of water ice at the lunar poles. So, as the mission neared its end, it was decided to "use" the crash of Lunar Prospector as part of an experiment in order to confirm the existence of water on the Moon. The spacecraft was successfully directed into a crater near the lunar south pole, thought to be a likely location for ice deposits. Unfortunately, the analysis of the experiment, detected no indication of water. In any case, the mission successfully completed all of its objectives and the data from it was 10 times better than hoped and much better than any data ever collected.