Chicago Public School's CEO Barbara Byrd-Bennett has resigned amid a federal probe of a $20 million no-bid contract between the district and a training academy where she once worked as a consultant, officials said.

In a short letter released by the school district, Byrd-Bennett notified David Vitale, the president of the board of education, that she was submitting her resignation, effective Monday.

"I remain forever thankful for the opportunity to serve the children of Chicago and the District," she wrote.

Neither that letter nor subsequent statements released by Mayor Rahm Emanuel and Vitale discussed the investigation that prompted Byrd-Bennett to take a paid leave of absence from her position with the nation's third-largest school district.

But Emanuel alluded to the investigation.

"I am saddened by the circumstances that have led to Barbara's resignation and I wish her well," Emanuel said in a two-sentence statement released by his office Monday.

Her attorney, Michael Scudder, declined to comment, citing the pending investigation.

Byrd-Bennett, who has not been accused of any wrongdoing, took her leave of absence in April following reports that federal investigators were looking at the contract between CPS and SUPES Academy. A spokesman for the academy said it has turned over records to investigators, who have also asked for documents from Byrd-Bennett and three other employees. CPS has suspended its contract with SUPES.

Immediately after the school district confirmed that it had been served with federal grand jury subpoenas, Emanuel said his office was not involved in the awarding of the SUPES contract. But the Chicago Tribune subsequently reported about a lengthy document on SUPES letterhead that was emailed in September 2012 to Emanuel's top education adviser, Beth Swanson, his then-deputy chief of staff.

On Monday, the Tribune reported that SUPES officials boasted in documents emailed to City Hall about the academy's influence with the mayor's office, even saying that it was "heavily involved in the recruiting the current Chief Executive Officer, both the former and current Chief Education Officer, and the current Chief of Staff."

A longtime educator, Byrd-Bennett earned a salary of $250,000 and has ties to school systems in New York, Detroit and Cleveland. Emanuel chose her in 2012 to lead the district.

Chicago Board of Education Vice President Jesse Ruiz has served as interim CEO since April and, according to Vitale's statement, he will continue in that role. He's an attorney and a former chairman of the Illinois State Board of Education.

The investigation comes at a critical time for the district, which faces a roughly $1 billion budget shortfall and a severely underfunded pension system. Contract negotiations with the powerful Chicago Teachers Union are coming up this year. During the last round in 2012, Chicago teachers went on strike for the first time in 25 years.