The state board denied the school's appeal Wednesday to keep control of its two remaining campuses in Bronzeville and Englewood.
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"The decision reached today was not an easy one to make, and the powerful testimony we heard throughout the process did not fall on deaf ears," officials said.
The state board said Urban Prep was poorly run and not financially responsible in recent years, saying it did not have the best interest of students in mind.
School leaders disputed those claims during Wednesday's meeting.
The board pointed to recent investigations involving the charter school, as a report from the Chicago Public Schools inspector general included misconduct allegations against the charter school's founder, Tim King.
Parents picking up students from school Wednesday said they're disappointed to see it end like this.
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"It's a little bothersome. I wish they would've gave the new principal a chance to turn the school around," said Ena Jones, the parent of freshman.
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"I am confident that each of you, as as students, will continue to have an extremely bright future," ISBE officials said.
CPS will now permanently control the academies, saying it will not close the two campuses, in Englewood and Bronzeville, and the district hopes to retain all teachers and staff.
But some parents said they're considering private school.
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"It was more things geared toward their personal legends and their personal aspirations. I don't think he can get that through Chicago Public Schools," Jones said.
Urban Prep released a statement Wednesday, saying,
"We are very disappointed that the Illinois State Board of Education has denied our appeal of the Chicago Public Schools Board of Education's decision to close Urban Prep. Nevertheless, we remain committed to ensuring that Urban Prep and the thousands of students it has served remains open. To that end, Urban Prep Academies has filed a lawsuit in the Circuit Court of Cook County asserting that the Chicago Public Schools has violated state law that there be a moratorium on school closings until 2025. We trust that the courts will rule in favor of justice and Urban Prep students and families.
"Further, we are asking the Illinois General Assembly and Mayor-elect Johnson to intervene to stop the dismantling of Urban Prep Academies. It's important to note how high the stakes are. If the courts or elected leaders do not step in, the nation's first network of charter high schools for boys and Illinois' only all-boys public schools, will cease to exist.
"Further, Urban Prep has had an unparalleled level of success for its students. Urban Prep's 90% high school graduation, for example, dwarfs CPS's 65% high school graduation rate for Black males. Across every metric, Urban Prep outperforms Chicago Public Schools for our demographic, which makes the CPS and ISBE decisions even more confounding."