One of the jurors who wanted to acquit, a 68-year-old Northeast Philadelphia woman named Shirley, who did not want to give her last name, said afterward: "I had substantial reasonable doubt and I didn't think there was any intent to defraud."
Assistant U.S. Attorneys Joan Burnes and Frank Costello said the prosecution "absolutely" plans to retry Brown on the deadlocked counts.
Brown founded Laboratory Charter School, Ad Prima and Planet Abacus, all in Philadelphia, and also helped set up Agora Cyber Charter on the Main Line.
Brown, who smiled after all the jury's decisions were read in court, declined to comment afterward. Her husband, William H. Brown III, a former member of the city Board of Ethics, had resigned from the board a month after his wife was indicted in 2012, telling Mayor Nutter he planned to devote himself "to restoring the excellent reputation my wife, June, enjoyed until recently," the Inquirer has reported.
William McSwain, one of Brown's attorneys at Drinker Biddle & Reath, said Brown was "certainly happy she hasn't been convicted of anything, but naturally would have preferred the jury to reach a verdict on all the counts."
One juror, Christine Dick, 55, of Malvern, said, "I think three people had their minds already made up" to acquit Brown before the deliberations even started.
She thought Brown should have been convicted on the deadlocked charges. "I was very clear in how I felt," she said, adding, "I can say I thought the prosecution did a phenomenal job."
She and another juror, Lauren Quinty, 30, of Montgomery County, both told the judge when they were individually polled in the courtroom that they "sadly" agreed that the panel was hopelessly deadlocked on 54 counts.
Rosemarie Schaffner, 57, of Bucks County, also said she thought there was "a lot of evidence" to convict.
Brown was acquitted of four counts of wire fraud centering on a $205,500 implementation grant from the state for Agora Cyber. She was also acquitted of one count of obstruction of justice and of a sole count of witness tampering regarding the testimony of a charter-school employee.
The 54 counts the jury deadlocked on were wire fraud and obstruction-of-justice charges.
After a five-week trial, the jurors on Dec. 19 had acquitted Brown's two codefendants, Michael Slade Jr. and Courteney Knight, but said they were split on the charges against Brown.
Jurors then returned Wednesday to deliberate on Brown after a holiday break.
On Twitter: @julieshawphilly