The girl was attacked in a forest in Sollentuna, to the north of the capital, at around 2pm on Tuesday.
“The girl was lured into a car and driven to the Sjöberg area where he raped her,” said Diana Sundin, spokeswoman for Stockholm police.
Following the attack, the girl ran home and told her parents what had happened. She was undergoing a hospital examination on Tuesday afternoon.
Police are asking for witnesses who saw the man, who was driving a dark-coloured car.
“We don’t want to release a description at the moment, as this is information from a small child,” Sundin said.
The man’s approach to the girl differed substantially to the methods used by a paedophile who has molested some twenty children in Stockholm over the past year, and who has so far not been caught.