After serving as president of Girard College for five years and helping stabilize its finances, Clarence "Clay" D.  Armbrister will step down in December to become president of Johnson C. Smith University, a historically black college in Charlotte, N.C.

The Board of Directors of City Trusts, which oversees the Girard Estate, announced Armbrister's resignation Wednesday with "deep regret."

Armbrister, 60, presided at a time when there was contentious debate over the future of the programs that would be offered at the unusual boarding school for low-income students in North Philadelphia. He also led an academic restructuring of the school.

Ava Willis-Barksdale, Girard's vice president, will become interim president while the board launches a search for Armbrister's permanent successor.

"Clay has done a tremendous job as president of Girard College, and we are grateful for his outstanding service to Girard and to the children of our city," board president Ronald Donatucci said in a statement. "We will miss him, and we wish him the very best as he takes on this new role."

Armbrister's departure comes as the board is launching a planning process for Girard's future.

The school, which provides a college-prep education, has 305 students from first through 12th grades on its leafy campus at 2101 S. College Ave., just off Girard Avenue.  Students live on campus during the week and go home on weekends.

Prior to arriving at Girard, Armbrister, a lawyer, held leadership positions with the Philadelphia School District and Temple University and was a mayoral chief of staff during Michael Nutter's first term. He also served as a senior vice president and chief of staff at Johns Hopkins University in Baltimore.

"I am looking forward to this new opportunity, which is something I've always wanted to do, but this is bittersweet for me," Armbrister said.  "I love Girard College and what it stands for, and I have been truly blessed to work with such an outstanding community of students, teachers, administrators, alumni, and the entire Girard Family."

He said he began thinking about leading a college or university while working at Temple.

"It reflected so much the city in which we live  in — the diversity of the school, and it just reinforced what I had always known: Places of higher education are not only where education is taught but discovered," he said. "It's a powerful place to be."

Merchant and banker Stephen Girard's 1831 bequest created the free boarding school for poor orphans on the 43-acre site in Fairmount.

The board provoked an outcry in 2013 when it petitioned Orphans' Court to change conditions of Stephen Girard's will to temporarily end the boarding and high school programs to cut costs, replenish shrinking reserves, and avert financial ruin.

An Orphans' Court judge ruled the secondary and boarding programs were critical parts of Stephen Girard's vision and denied the petition. Commonwealth Court upheld the decision.

Ronald Marrero, president of the Girard Alumni Association, wished Armbrister well, adding: "We always greatly appreciated that he kept open the lines of communication and the working relationship we had, despite the fact that we were in opposition to the board's position to modify the school."