The indictments, which were unsealed Thursday, came nearly two years after The Inquirer first reported allegations of fiscal mismanagement and conflicts of interest at the school, which has campuses in the Stenton and Germantown neighborhoods.
Joan E. Burnes, an assistant U.S. attorney who is prosecuting the case, said that between March 2005 and December 2009, Walker and Clark allegedly stole more than $500,000 in taxpayer funds that were meant to educate students at the charter school.
Clark was the president of the charter's board and Walker was the school's chief executive officer. Both were involved in founding the school in 2004.
New Media is the fourth Philadelphia charter school in recent years whose administrators or board members have faced federal fraud charges. And the school is among at least 18 area charter schools that have come under federal investigation since 2008, sources have said.
The Philadelphia School Reform Commission forced Walker and Clark to step down and sever all ties to the school as conditions for renewing New Media's operating charter in 2010. The SRC also required all members of the charter board to be replaced. That overhaul was completed in July.
Under state law, the district that awards a school's operating charter is responsible for overseeing it. New Media is one of 74 charter schools operating in the school district.
Under its new leadership, the charter enrolls 455 students in grades five to 12.
Clark, a lawyer, who was arrested Thursday morning, was released on a $25,000 recognizance bond after making an initial appearance before U.S. Magistrate Thomas J. Rueter later in the day.
During the brief proceeding, Clark told Rueter that he would retain his own attorney but had not had an opportunity to do so.