Jeffrey S. Flier, an expert on obesity and diabetes, will take over on Sept. 1 as the permanent dean of Harvard Medical School, University President Drew G. Faust announced Wednesday.

Flier, a 29-year veteran of Harvard, is currently the chief academic officer at the Harvard-affiliated Beth Israel Deaconess Medical Center.

His appointment came after a nine-month search that seemed to be nearing an end in late May, when Elizabeth G. Nabel, director of the National Heart, Lung, and Blood Institute and reportedly a top candidate for the Medical School deanship, traveled to Cambridge for a series of search-related meetings. But several weeks after Nabel's under-the-radar visit, Faust named Barbara J. McNeil, a professor of health care policy, to lead the school on a temporary basis while Faust rushed to find a permanent leader.

Flier was a founding member of the Harvard University Science and Engineering Committee (HUSEC), a group focused on improving University-wide science initiatives. Faust, in her first few months since being named president, has already emphasized her desire to bring Harvard's 10 schools closer together through University-wide initiatives like the science planning led by HUSEC.

"[Flier's] outlook and experience will position him well to build on the remarkable strengths of our Medical School, to strengthen cooperative efforts within the broader Harvard medical community, to pursue important new opportunities for fruitful connections with other parts of the University, and to speak more broadly to medical and health issues of national and international concern," Faust said in a statement.

As dean of the Medical School, Flier will have to seek out new methods of funding to respond to tight federal research budgets and also consider how to make the most of the school's expansion into Allston.

He will also build upon the legacy of Joseph B. Martin, his predecessor, who led the school for the past decade and oversaw its massive physical growth.

“Joe Martin has capably set the stage for the next evolution of Harvard medicine and I thank him and my many colleagues and friends on the faculty for their support. I know that together there are few things that we cannot accomplish,” Flier said in a statement.

Martin announced plans to step down last fall and officially left the position on June 30. He intends to continue to teach neurobiology at the Medical School.

Flier is the second permanent dean Faust has named since being named Harvards 28th president in February. In June, Faust tapped Michael D. Smith to lead the Faculty of Arts and Sciences. She has also appointed a number of interim leaders to fill the many administrative vacancies across the University.

The dean of Harvard Medical School oversees 11,000 faculty members at the school and 18 affliated institutions, which combined received over one billion dollars in federal funding for research last year.

—Staff writer Claire M. Guehenno can be reached at guehenno@fas.harvard.edu.