The "deep ocean under the icy crust of Ganymede opens up further exciting possibilities for life beyond Earth," said John Grunsfeld, an administrator with NASA.
NASA estimates the ocean is buried underneath a 150-kilometre-thick crust of ice and is 10 times deeper than Earth's oceans.
Ganymede, the largest moon in the solar system, is nearly 630 million kilometres from Earth.
Scientists discovered the presence of the ocean after noting that the moon's magnetic field was interacting with Jupiter's magnetic field.
By observing the cyclical rocking of Ganymede's aurorae - ribbons of glowing gas near the moon's north and south poles - scientists were able to deduce that below the moon's surface lies a large body of salt water that is affecting Ganymede's magnetic field.
As early as the 1970s, scientists theorised that an ocean could be hiding below Ganymede's surface.
Evidence for the discovery was provided by NASA's Hubble Space Telescope, which orbits around the Earth and above its atmosphere at nearly 8 kilometres per second.
The announcement comes a month before NASA celebrates 25 years of discoveries made by the Hubble Space Telescope.
It was launched into low Earth orbit in April 1990.