The new alleged victim, referred to as Minor Six, was included as part of an updated federal indictment.
Prosecutors also said they had seized more than 100 electronic devices, such as smartphones, iPads and hard drives, after executing a search warrant.
The judge set a trial date for 13 October, six months later than planned.
The Chicago case includes several counts accusing Kelly of child pornography. The chart-topping US singer, whose full name is Robert Kelly, has consistently denied the allegations.
The updated indictment is largely the same as the original - which also had 13 counts - but now includes a reference to Minor Six.
Prosecutors offered little detail about the new alleged victim, but said the person met Kelly in the late 1990s at the age of 14 or 15.
The indictment said Kelly "engaged in sexual contact and sexual acts" with Minor Six and four others when they were aged under 18.
The R&B singer is facing several state and federal charges of sexual abuse in the US.
Kelly was arrested in Chicago in July on two sets of charges including sex trafficking, child abuse images and obstruction of justice.
He has already pleaded not guilty to more than 20 sexual offences across several US states, including prostitution charges in Minnesota.
The allegations were brought back into the spotlight following the documentary series, Surviving R. Kelly, which aired in the US at the start of 2019.
It detailed stories about him pursuing teenage girls going back to the start of his career.