In an indictment returned Wednesday by a federal grand jury, Tim King is accused of stealing the money in 2021 and 2022 to allegedly pay for personal credit card charges.
Prosecutors also say he deleted online records, after learning a criminal investigation was underway.
King, 59, of Chicago led Urban Prep until 2022, when he was forced out after the misconduct allegations first surfaced.
He's been charged with federal program theft and obstruction of justice.
Arraignment in U.S. District Court in Chicago has not yet been scheduled.