Spanier, accompanied by his wife, signed paperwork after his bail was set at $125,000 unsecured and left a Harrisburg district justice's office where two co-defendants were arraigned last week.
After the court appearance, Spanier's attorney, Elizabeth Ainslie, proclaimed Spanier's innocence and called prosecutors' claims he was part of a conspiracy of silence "ridiculous."
Spanier, 64, was charged last week with perjury, obstruction, endangering the welfare of children, failure to properly report suspected abuse and conspiracy for his actions in response to complaints about Jerry Sandusky showering with children. Spanier denies the allegations and has claimed he is being framed for political purposes.
He served as Penn State's president for 16 years but was forced out a year ago after Sandusky was charged along with two of Spanier's top underlings. Spanier is on paid leave as a member of the faculty.
Along with the charges against Spanier, prosecutors added counts against Tim Curley and Gary Schultz. They were arraigned Thursday. Curley, the athletic director on leave, and Schultz, the school's retired vice president, await trial in January on charges of failure to report suspected abuse and perjury.
The new charges came almost exactly a year after details of the case against Sandusky sent a maelstrom through State College, toppling longtime head coach Joe Paterno and eventually leading to severe NCAA sanctions against the football team.
Sandusky, 68, vigorously contested the charges but was convicted in June of 45 counts of abuse of boys, including violent sexual attacks inside campus facilities. He was sentenced last month to 30 to 60 years in prison.
A grand jury report alleged Spanier testified falsely that he did not know of a 1998 complaint against Sandusky, made by a mother and investigated by university police.
"Spanier was obviously kept in the loop on this matter as Schultz copied him in on emails that discussed the status and conclusion of the investigation," the jury report said.
It also claimed Spanier lied, about a 2001 instance of abuse witnessed by a graduate assistant, when he testified that Curley and Schultz described it only as horseplay. Email traffic among the men, jurors wrote, "make clear they are discussing an event that involves the abuse of a child."
Spanier's obstruction charges involve "numerous lies" and hiding "pertinent files and notes," alleged the grand jury report, known as a presentment.
The report described how he addressed the growing scandal last year with the board of trustees, and how he put out statements supportive of Curley and Schultz after their arrest. The jury report said investigators were immediately able to get important records from the university after Spanier was replaced as president.
"It should be noted that Spanier continues to mislead with numerous public statements that contain demonstrably false statements," the jury claimed.
Spanier's lawyers put out a written statement law week that accused Gov. Tom Corbett, who was attorney general when the investigation began, of orchestrating the charges to divert attention from questions about why it took three years to bring charges against Sandusky. They said there was no factual basis for the Spanier charges.
"Spanier has committed no crime and looks forward to the opportunity to clear his good name and well-earned national reputation for integrity," his defense lawyers wrote. "This presentment is a politically motivated frame-up of an innocent man."
Attorney General Linda Kelly said last week the three administrators had engaged in a "conspiracy of silence" to hide the truth.