Secretary of the Faculty of Arts and Sciences (FAS) David B. Fithian will leave his post at Harvard for one of the top administrative jobs at the University of Chicago, where he will report directly to the school’s president and Board of Trustees.

Fithian, who has spent 12 years at Harvard and is also an associate dean of FAS, will assume his duties as secretary of the University of Chicago on July 1.

Fithian’s departure comes at a time of significant reshuffling within the Harvard administration.

President-elect Drew G. Faust is set to take the helm this summer, and she has yet to announce who will lead FAS and its Graduate School of Arts and Sciences (GSAS) when she takes office. The current FAS and GSAS deans plan to step down at the end of the academic year.

Fithian, who said that Chicago first contacted him in late March, called his new job “an extension of the work I’m doing now.”

“It seemed like a natural next step,” Fithian said in a phone interview yesterday. “I’ve spent my entire life in the Northeast so a new city and a new job and a new university seemed like an exciting opportunity.”

Robert J. Zimmer, who is finishing his first year as Chicago’s president, said in a press release that his university was looking forward to benefiting from Fithian’s expertise.

“At Harvard, where he has been for 12 years in a series of progressively more responsible positions, he became known for his wise counsel on governance and process and his thoughtful, calm judgment on even the most difficult issues,” said Zimmer, who received a PhD in mathematics from Harvard in 1975.

Fithian said yesterday that he and his husband, Michael Rodriguez, have bought a house in Chicago and that the university is looking to find a job on campus for Rodriguez, who taught the popular Harvard class Psychology 1703, “Human Sexuality.”

In his present capacity as FAS secretary, Fithian acts primarily as the link between the FAS dean and the Faculty Council, the Faculty’s 18-member governing body.

Theda Skocpol, the outgoing GSAS dean, said that Fithian’s departure “is a very serious loss for Harvard, because he is knowledgeable, open to ideas, works cooperatively with everybody, but he manages to help the business of the Faculty move along.”

“The new dean is going to be in trouble without his services,” she added.

Interim Dean of the Faculty David Pilbeam, who took on the interim post at the end of last month, said that Fithian and his professionalism will be missed.

—Staff writer Alexandra Hiatt can be reached at ahiatt@fas.harvard.