The incident is said to have taken place in Torsås, a small town south of Kalmar. It was the boy's mother who reported the matter to the police, claiming that her son was attacked by four girls as he made his way home.
The girls are thought to have been the same age as the alleged victim and at least one is reported to have known the boy.
"This is a small town so it's very probable that they knew each other," police spokesman Sven-Erik Karlsson told TV4.
Police said it was unusual, though not entirely unheard of, for boys to be raped by girls.
"It is a bit of a reversal of what we are used to. But we don't really know what happened yet. We have launched a preliminary investigation," Karlsson told Östran.
The boy also reported that he was assaulted by two boys his own age later on Monday evening.
"He was beaten by two unknown perpetrators," Karlsson told TV4.
The boy's mother said that he had also received threats on Lunarstorm, a community website for young people.
As the boy has not yet turned 18, police are treating the report as a juvenile case.
"We usually give cases like this priority," Karlsson told Östran.