The Norwegian police did not reveal where they found the painting, which was stolen along with another Munch artwork, Madonna, but said both were recovered on Thursday afternoon in "pretty good condition".
"For two years and nine days we have been hunting systematically for these pictures and now we've found them," said Iver Stensrud, head of the police investigation.
"It is a happy day for us in the police, for the owners of the paintings, and not least for the public, which will soon be able to once again admire the paintings."
Norwegian-born Munch, who died in 1944 aged 80, was one of the founding fathers of the Expressionist movement. He made several versions of both artworks, with The Scream regarded by many as his most important work.
Oslo's Munch Museum also expressed delight over the national treasures being recovered.
"I am almost crying from happiness," said Gro Balas, who chairs the Munch Museum board.
"They have been given a cursory examination, but for now I am content just to feel overjoyed."
The Scream and Madonna were stolen in August 2004, when two hooded men stormed into the Munch Museum in Oslo and threatened a staff member with a gun before stealing the painting and escaping in a getaway car.
The two gunmen remain at large, although in May this year three men were sentenced to prison for their involvement in the theft.
The driver of the getaway car, Petter Tharaldsen, was sentenced to eight years in jail, while Bjoern Hoen, accused of being one of the masterminds of the theft, was given seven years.
Petter Rosenvinge was sentenced to four years for complicity in the theft.
Tharaldsen and Hoen were also fined $122m after the prosecution called for the fine to be as high as possible to entice the men to reveal where they had hidden the paintings.
Investigators' progress was hampered by the thieves' skill in covering their tracks, such as setting off a fire extinguisher in the getaway car to erase all traces of their DNA, prosecutors said.
Although the paintings were believed to be too well-known to be sold on the open art market, Norwegian officials had issued a $315,000 reward for their recovery.