Citing court documents, news outlets report that 53-year-old Mike Ulmer was charged last week with two counts of rape and one count of sexual assault.
Ulmer is the pastor of Bethlehem Baptist Church in Henderson.
Authorities say Ulmer picked the Chester County High School student up from school Feb. 16 and brought her to his home.
The teenager told investigators Ulmer tied her hands together inside his office and sexually assaulted her.
Chester County Director of Schools Troy Kilzer says Ulmer, who worked with the in-school suspension program, has been suspended without pay.
Ulmer pleaded not guilty Tuesday and was released on bond.