The R&B singer was handed the charges in Cook County on Friday morning.
According to records, his first court date has been listed for March 8.
Sources tell the newspaper that Cook County prosecutors appeared before a judge on Friday afternoon to sign off an arrest warrant for Kelly.
R Kelly has denied all allegations made against him.
It comes after reports that he could face criminal charges over a sex tape that allegedly showed him engaging in intercourse with a 14-year-old girl.
Although, it is not known if the charges that have been brought against him are connected to the alleged tape.
It was said that a video showing the alleged act between Kelly – who has denied all allegations – and an underage girl is now in the hands of US prosecutors.
And it was said that a grand jury had been convened in Chicago to look at potential criminal charges for sexual misconduct, that could be brought against the singer, who is the subject of explosive six-part documentary Surviving R Kelly.
A source close to the case has reportedly confirmed to Business Insider that the jury met last week to begin their consideration of criminal charges against Kelly over the tape.
Celebrity lawyer Michael Avenatti says the video allegedly shows Kelly “engaging in multiple sexual assaults of a girl underage”.
It’s also alleged that the girl who features in the tape, which CNN says they have seen, refers to her body parts as being 14 years old.
It was passed to the Hollywood lawyer by a “whistleblower”, it’s said, before being handed to prosecutors in Chicago.
Authorities in Chicago are said to be already investigating claims made in the Surviving R Kelly documentary, which saw several women make allegations of sexual abuse against the singer.
This new tape allegedly shows 43-minutes of explicit scenes featuring a man, who CNN say appears to be Kelly, performing multiple sex acts with the girl.
She allegedly calls him “daddy” multiple times.
The media company also says the man asks the girl to urinate before her urinates on her.
Mr Avenatti says his client knows both Kelly and the girl in the video.
He said: “He identified the two of them on the videotape. He worked for and has known R. Kelly for decades and he met the girl on a number of occasions.”
Kelly’s attorney, Steven Greenberg, told The Sun: “This morning I woke up to reports that a video had surfaced showing R Kelly allegedly with an underage girl.
“The reports were prompted from a tweet by Michael Avenatti, who himself was the subject of unfavourable news articles just yesterday. Timing is everything.
“The calls and emails I received were the first I’ve heard of these allegations. I understand that CNN says that they have seen this video.”
He adds that he has not been contacted by law enforcement, and that Kelly hasn’t either.
He also says Kelly denies that he engaged in any illegal conduct.
Greenberg also says that Kelly has been “adjudged guilty in the public eye” because of a “documentary that regurgitated long ago rejected claims”.
The alleged tape did not appear in evidence in Kelly’s 2008 trial in which he was acquitted on child pornography charges.