Spanier is accused of covering up child molestation allegations against former assistant football coach Jerry Sandusky. Spanier becomes the third college official charged in the alleged cover-up.
Prosecutors also added counts against athletic director Timothy Curley and Vice President Gary Schultz, who were charged last year with lying to the grand jury and failing to properly report the allegations.
Spanier, 64, was charged with perjury, obstruction, endangering the welfare of children and conspiracy. Curley and Schultz face new charges of endangering the welfare of children, obstruction and conspiracy.
Sandusky was convicted in June of sexually abusing 10 boys over 15 years. He is now serving a 30- to 60-year sentence in prison. Spanier's attorneys insisted he was never told there was anything of a sexual nature involving Sandusky and children.
Spanier had been university president for 16 years, but he was forced out of his position after Sandusky's November 2011 arrest.
The Associated Press contributed to this report.