After five weeks of testimony, and seven days of deliberations, jurors in January acquitted the veteran educator on six counts and deadlocked on the remaining 54.
Jurors said afterward the panel was split 9-3 in favor of convicting Brown.
Two former charter administrators were acquitted of conspiracy and obstructing justice.
Two other former administrators pleaded guilty before the trial began and testified against Brown during the trial. Both are awaiting sentencing.
After the trial ended, defense attorneys asked Surrick to drop all charges against Brown, saying prosecutors had failed to prove their case.
Prosecutors countered that there was plenty of evidence to convict Brown, including forged documents and testimony from former charter employees.
Brown founded three elementary charter schools in the city that have been academic successes: Laboratory, which has campuses in Northern Liberties, Overbrook, and Wynnefield; Ad Prima, with campuses in Overbrook and Frankford; and Planet Abacus, in Tacony.
She also helped found Agora Cyber Charter in 2005 but cut her ties with it four years later as part of a settlement involving several civil suits, including one with the state Department of Education. Agora continues under a new administration in Wayne.