The R&B star, whose real name is Robert Sylvester Kelly, has faced claims of sexual abuse against women and teenage girls for decades.
He has never been convicted and has previously denied all the allegations.
The 52-year-old is expected to appear in court in Chicago, where he lives, on 8 March.
According to United States media who have seen court records, there are four alleged victims, who were aged 13 to 16 at the time of their reported assaults.
Kelly's lawyer told the Chicago Sun-Times he had not yet been notified of the charges against his client but said R Kelly denied any wrongdoing.
Last week, lawyer Michael Avenatti said that his office had uncovered previously unreleased footage of Kelly having sex with a young girl. The footage was then handed to the Cook County State Attorney, whose jurisdiction includes Chicago.
There have been calls in recent months to boycott Kelly's music - both recordings and performances - with negative messages posted on social media using the hashtag #MuteRKelly.
Kelly, best known for hit song I Believe I Can Fly, has faced numerous accusations of sexual misconduct, making indecent images of children and other offences.
The singer is the subject of the documentary Surviving R Kelly, which premiered in New York in December and featured women who accuse him of sexual and physical abuse.
In 2017, Kelly denied allegations that he was holding a number of young women captive in a so-called "abusive cult".