Mayor Michael Nutter and Gov. Ed Rendell, who appoint the commission members, announced the selection at a news conference.
They acknowledged that Ackerman left her post in San Francisco after conflicts with the school board, but called that a sign of someone who stood up for what is right.
"If you show me a big-city school superintendent whose never had a run-in," Nutter said, "I'll probably try to show you someone who never tried to accomplish something."
During five years in San Francisco, Ackerman was credited with boosting test scores and addressing the achievement of minority students. But she left in June 2006 after clashing with three board members who criticized her leadership style.
In May 2000, she left her position in Washington after two years in which she repeatedly criticized the structure of the system. She was credited with attracting new teachers, raising test scores and erasing a $62 million deficit in less than a year.
In her new post, Ackerman enters a school district where nearly half of the students drop out before graduating. The district has made strides in the six years since a state takeover that replaced the school board - math and reading scores increased more than 20 percent between 2002 and 2006 - but many students are still failing.
Ackerman, who has taught at Teacher's College of Columbia University since September 2006, was not at Tuesday's announcement because her father was ill.
"I am coming back to active leadership because I have missed my passion - the on the ground battle for our children who attend urban public schools," she said in a statement. "I believe I still have more to give in this important fight for social justice."
The district has been run by the five-member School Reform Commission since a state takeover of the financially and academically troubled district in December 2001.
The takeover came after state lawmakers grew fed up with high dropout rates and low test scores plaguing the system. The state created the School Reform Commission to replace the school board, with the governor appointing three members and the mayor picking two.
The effort began one of the largest school privatization experiments in the country. Edison Schools was one of seven companies, universities and nonprofit groups hired to run the city's worst-performing schools.
Vallas, the former superintendent, stepped down in June to head the rebuilding New Orleans schools. Interim CEO Tom Brady has been in the post since then.
Commission member Martin G. Bednarek said he hoped Ackerman could start within the next month, but that details were still being worked out.
