Prosecutors say the Rev. Charles Newman used some of the money to pay a student he allegedly molested with drugs and alcohol.
Newman is a former principal at Archbishop Ryan, the largest high school in the Philadelphia archdiocese.
City prosecutors say he stole about $330,000 from the high school and $550,000 from his religious order, the Franciscan Friars.
The 58-year-old Newman and defense lawyer Frank DeSimone declined comment after the brief hearing Wednesday.
Newman now lives at a Franciscan retirement home in Wisconsin.