The girl was dragged into a toilet at the public library at around 2.30pm on Tuesday afternoon when her mother wasn't looking and is alleged to have been subject to a rape by a male assailant.
The details of the case remain uncertain as police are reluctant to divulge any information due to the alleged victim's young age.
"According to witnesses the man and the girl were in the toilet for a short time. Exact what happened in there will have to be established by the police investigation," said Lotta Thyni at Södertälje police to the Aftonbladet daily.
The girl was taken to hospital and is reported to have sustained minor injuries and she has been able to provide police with a description of the man.