That complaint surfaced last week, but police say 28-year-old Todd McCullough, of Kiski Township, raped the Saltsburg High School student in April.
McCullough doesn't have an attorney and declined to comment after his arraignment Thursday on rape and related charges. He remains in jail pending a preliminary hearing Nov. 13.
The school district says it's been cooperating with police since an internal investigation determined the employee violated state law and district policies.
Trooper John Matchik says police consider the investigation "intense and ongoing."
Saltsburg is about 30 miles east of Pittsburgh.