Lunar Prospector was the third mission selected by NASA for full development and construction as part of the Discovery Program. At a cost of $62.8 million, the 19-month mission was designed for a low polar orbit investigation of the Moon, including mapping of surface composition including lunar hydrogen deposits, measurements of magnetic and gravity fields, and study of lunar outgassing events. The mission ended July 31, 1999, when the orbiter was deliberately crashed into a crater near the lunar south pole, after the presence of hydrogen was successfully detected.

The Discovery Program is a series of Solar System exploration missions funded by the U.S. National Aeronautics and Space Administration (NASA) through its Planetary Missions Program Office. The cost of each mission is capped at a lower level than missions from NASA's New Frontiers or Flagship Programs. As a result, Discovery missions tend to be more focused on a specific scientific goal rather than serving a general purpose.