Astronomers claim that the water was delivered by comet Shoemaker-Levy 9, which collided with the planet in 1994.
The water is particularly concentrated where the comet entered the planet's atmosphere.
Water at the bottom layers of its atmosphere is easily explainable but upper level atmosphere water was not until now.
Scientists figured that because one of Jupiter's hemisphere's has water and the other doesn't, a single event like a comet must explain it.
"The asymmetry between the two hemispheres suggests that water was delivered during a single event and rules out icy rings or moons as candidate sources," said study author Thibault Cavalie of the Laboratoire d'Astrophysique de Bordeaux in France.
"Local sources would provide a steady supply of water, which over time would lead to a hemispherically symmetric distribution in the stratosphere. According to our models, as much as 95 percent of the water in the stratosphere is due to the comet impact."