The Second Mile's board of directors said in a statement Monday that it had accepted the resignation of Dr. Jack Raykovitz.
Raykovitz, a practicing psychologist, had testified before the grand jury that indicted Second Mile founder Jerry Sandusky on 40 counts of child abuse. The grand jury said Sandusky, a former Penn State assistant football coach, found his victims through the charity's programs.
The board also said that would conduct an internal investigation to assess policies and make recommendations regarding future operations. They hope to have those findings by the end of December.
Raykovitz said in a statement Monday that he hopes his resignation would mark the beginning of a "restoration of faith in the community of volunteers and staff" at The Second Mile.
Sandusky founded The Second Mile in 1977. The group has said that its youth programs serve as many as 100,000 children a year.
Sandusky, who retired from Penn State in 1999, informed The Second Mile board in November 2008 that he was under investigation. The charity subsequently barred him from activities involving children, charity officials said.
The ex-coach is accused of assaulting eight children over a 15-year span. His attorney has said he's innocent.
Penn State Athletic Director Tim Curley and Senior Vice President Gary Schultz were charged with perjury. Both have denied wrongdoing and have left their university posts.
The scandal led to the departure of university President Graham Spanier and the dismissal of legendary head coach Joe Paterno after law enforcement officials said they didn't do enough to stop suspected abuse when it was reported to them in 2002.