Spanier, who resigned as president after the Sandusky scandal broke, faces charges of conspiracy, obstruction, perjury and child endangerment.
While Spanier said little as he left the hearing in Harrisburg, his attorney, Elizabeth Ainslie, called the charges "ridiculous," The Philadelphia Inquirer reported.
Prosecutors allege Spanier was part of a "conspiracy of silence" that attempted to cover up allegations against Sandusky, the university's former football defensive coordinator.
They allege Spanier, suspended Athletic Director Tim Curley and former Penn State vice president Gary Schultz ignored accusations against Sandusky as early as 1998.
The 68-year-old Sandusky has been convicted and sentenced to at least 30 years in prison.