Embattled Chicago Public Schools CEO Barbara Byrd-Bennett has resigned in the wake of the federal probe of a $20.5 million no-bid contract CPS handed her former employer, the mayor’s office announced Sunday night.

Byrd-Bennett went on paid leave in mid-April, days after federal investigators sent subpoenas to CPS seeking records about her, top aides she brought to Chicago and three companies owned by her former employers, Gary Solomon and Thomas Vranas.

Appointed to the city’s top schools job by Mayor Rahm Emanuel in the wake of a historic 2012 teachers’ strike, Byrd-Bennett was once employed by two of Solomon and Vranas’ firms, SUPES and Synesi. Had she not resigned, her contract with CPS would have allowed her to remain CPS’s $250,000-a-year CEO through June 30, 2016.

But in a brief letter to school board president David Vitale dated Friday, she ended her term, effective Monday. Byrd-Bennett wrote that she will “always be thankful for the opportunity to serve the children of Chicago.”

Neither Byrd-Bennett nor her attorney could be reached late Sunday for comment. Neither CPS nor the mayor’s office would say why they held the news until late Sunday.

District spokesman Bill McCaffrey said Byrd-Bennett’s paid time off was due to run out on June 5. She will be paid through Friday, he said.

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Vitale released a statement Sunday on behalf of the Board of Education saying that “interim CEO Jesse Ruiz will continue in that role to advance the important work of the Chicago Public Schools on behalf of our students, families, and communities across the City of Chicago.”

And Emanuel sent a statement saying he is “saddened by the circumstances that have led to Barbara’s resignation and I wish her well.

“As a city, our focus must remain on finishing the school year strong and tackling the billion dollar budget deficit that threatens the progress our students, teachers, principals and parents have made over the last several years,” he wrote.

His office would not say whether the mayor had anything to do with Byrd-Bennett stepping down.

Federal subpoenas asked for records from the district for Tracy Martin, Rosemary Herpel and Sherry Ulery, all longtime Byrd-Bennett cronies who moved to Chicago to work for CPS after Byrd Bennett took the helm.

All the other three women remain employed in their six-figure jobs at CPS, according to McCaffrey. CPS is footing the bill for their attorneys, though they have not been accused of any wrongdoing.

Byrd-Bennett’s resignation comes two years after she in June 2013 recommended that the Board of Education approve a $20.5 million no-bid principal training contract to SUPES Academy. Controversially, that recommendation came just two weeks after she permanently shuttered 50 neighborhood schools.

She apparently made a case for the Wilmette-based business that once employed her as a coach in Chicago, saying they offered a unique service, assigning superintendents from districts across the country as mentors for principals. But Chicago principals complained that the training wasn’t pertinent, nor were the mentors experts in running schools in a large urban district.

Vitale and interim CEO Ruiz were among the six members of Emanuel’s handpicked school board to approve the contract, through both have since tried to distance themselves from it. The SUPES deal was cancelled in April, though CPS has already paid more than $12 million of it so far.

Solomon was once a dean at Niles West High School, but left under a cloud after administrators alleged that he’d sent sexually inappropriate emails to students and also used racial slurs to describe an African-American administrator.

Dennis Culloton, a spokesman for SUPES Academy, has continued to defend the quality of the company’s training.

Barbara Byrd Bennett's resignation letter | (supplied)

Barbara Byrd Bennett’s resignation letter | (supplied)