The hearing for Gary Schultz and Tim Curley on charges of endangering the welfare of children, obstruction and conspiracy lasted about 10 minutes in a suburban Harrisburg courtroom. Bail was set at $50,000.
Afterward, Schultz attorney Tom Farrell talked of the positive things the men have accomplished, along with their co-defendant, former Penn State president Graham Spanier.
"People of this character do not do, have not done what they're charged with," Farrell said.
Curley and Schultz shook hands and greeted each other warmly inside the courtroom but said little during the proceeding, after which they drove away to be fingerprinted.
Spanier has been out of state at a relative's funeral and will be arraigned on Wednesday, the judge said.
The three men were accused in a withering 39-page grand jury report that was made public Thursday of conspiring to conceal complaints about Sandusky, which gave him time and access to molest more boys before his arrest nearly a year ago.
Prosecutors alleged the men decided not to alert police or child welfare authorities after getting a 2001 report of Sandusky sexually abusing a boy in a team shower.
Attorney General Linda Kelly said at a Capitol news conference Thursday that all three "knowingly testified falsely and failed to provide important information and evidence."
Spanier is charged with perjury, obstruction, endangering the welfare of children, failure to properly report suspected abuse and conspiracy. Curley and Schultz were first charged a year ago, with perjury and failure to report abuse. Trial on those counts is scheduled for January.
Spanier's lawyers asserted his innocence and described the new charges as an attempt by Gov. Tom Corbett to divert attention from the three-year Sandusky investigation that began under his watch as attorney general.
Corbett spokesman Kevin Harley called the defence statement the "ranting of a man who has just been indicted for covering up for a convicted pedophile."
Sandusky, who spent decades on the Penn State football staff and was defensive co-ordinator during two national championship seasons, was convicted in June of sexually abusing 10 boys over 15 years. He has maintained his innocence and is serving a 30- to 60-year prison sentence.
Curley, 58, is the athletic director on leave while he serves out the last year of his contract. Schultz, 63, has retired as vice-president for business and finance.
In a pair of pretrial motions filed this week regarding their earlier charges, Curley and Schultz both focused on the role played by Cynthia Baldwin, the university's then-chief counsel who accompanied them to their grand jury appearances. They argued charges should be dismissed, or grand jury testimony suppressed, because they believed Baldwin was representing them.
Baldwin's grand jury testimony was a key piece of the evidence used to support the new charges.
"We were stunned, we were flabbergasted that she would testify against our clients," said Curley's lawyer, Caroline Roberto.
Farrell said Baldwin, a former state Supreme Court justice, "has betrayed her clients, her profession and testified falsely."
Baldwin's lawyer Charles De Monaco referred a reporter to a statement issued this summer in which he defended her, saying she "at all times fulfilled her obligations to the university and its agents."
Spanier, 64, of State College, had been university president for 16 years when he was forced out after Sandusky's November 2011 arrest. He remains a faculty member but was placed on paid leave Thursday.