Hanna, the district's lead negotiator with the PFT during 2009 contract talks, will become chief of innovation for the New York City public schools.
"Tomas' dedication to the young people in this district has been invaluable to our efforts to decrease violent incidents and make our schools more personal for our students and their families," Ackerman said in a statement.
Since returning to Philadelphia in 2008 - he previously served under CEO Paul Vallas - Hanna had also been Ackerman's chief of staff and chief of school operations.
"He was always very responsive to the people in the community," said Michael Churchill, a lawyer with the Public Interest Law Center of Philadelphia. "He listened well and was seen as trying very hard to make things work.
Hanna is expected to start his new post in mid-July.
"I'm truly excited about the opportunity to work with the young people and parents in New York City," Hanna said in a statement. "As most of my colleagues can attest, I believe that the personalization is paramount when it comes to addressing the needs of students."
David Weiner, another former associate superintendent under Ackerman, left for New York a few months ago.