Christine Towers, 26, was in a Chester County court where she waived her preliminary hearing.
Investigators say the Phoenixville woman had a relationship with a 16-year-old boy at the school.
Towers is charged with institutional sex assault and other offenses.
Towers worked as a teacher's aide at Conestoga High School starting in 2014. She coached girl's soccer, track, basketball and softball in the district.
The student reported the incidents to authorities just days before her arrest in late April.
The victim also claimed Towers urged him not to tell police.
In a letter to parents sent shortly after Towers was arrested, Tredyffrin/Easttown School District Superintendent Richard Gusick writes:
"When those placed in positions of supporting our children are charged with violating a fundamental trust, it is deeply disturbing to us all. The welfare of our students remains a top priority. We will continue to support all students as this case moves through the criminal justice system."
Gusick's letter added that Towers had no prior criminal history when she was hired and there is no evidence any other students were victimized.
She resigned from all her positions with the district even before officials learned of the investigation.