Chalker had faced multiple counts that included conspiracy to obstruct justice and wire fraud. She changed her plea in a hearing before U.S. District Judge R. Barclay Surrick.
He scheduled sentencing for Jan. 29.
It could not be learned whether Chalker had agreed to cooperate with prosecutors and testify against Brown and the other defendants.
Joseph G. Poluka, Chalker's lead lawyer, declined to comment Tuesday on the terms of her plea because they are under court seal.
Patricia Hartman, a spokeswoman for the U.S. Attorney's Office, also declined comment.
Brown's trial is scheduled to begin Nov. 4.
Prosecutors say Brown and the others had attempted to thwart investigators by fabricating documents during a four-year federal probe and urging others to lie.
Brown, a former Philadelphia School District principal, founded three small kindergarten-through-eighth-grade charter schools in Philadelphia: Laboratory, which has campuses in Northern Liberties, Overbrook, and Wynnefield; Ad Prima, in Overbrook and Frankford; and Planet Abacus, in Tacony.
The others facing trial are Michael A. Slade Jr., Brown's grandnephew who had been the CEO at Laboratory, and Courteney L. Knight, a former Laboratory teacher who once served as CEO of Ad Prima.
The trio have pleaded not guilty.
In addition to the charters Brown founded in Philadelphia, in 2005 she helped create the Agora Cyber Charter School in Devon, which provides online, in-home instruction to students across the state. Both Chalker and Knight were listed as part of Agora's founding group in the cyber school's application to the state Department of Education.
Brown cut her ties with Agora in 2009 as part of a settlement involving several civil suits. Now based in Wayne, Agora operates under new leadership.
Chalker, a veteran educator and resident of Springfield, Delaware County, initially worked with Brown in 1989 at Main Line Academy, a private school for special-education students that Brown founded many years ago in Bala Cynwyd.
Chalker, who later became the CEO at Planet Abacus, is the second colleague of Brown's to plead guilty since a federal grand jury returned a 67-count superseding indictment in January.
In March, Anthony Smoot, Brown's former business manager, pleaded guilty to charges that he had conspired with Brown and others to obstruct justice during the federal investigation of the schools.
An initial grand jury indictment was returned against Brown and the four administrators in July 2012.