Melissa Bonkoski, 38, was a science teacher and softball coach at Owen J. Roberts High School. She was arrested earlier this month for inappropriate contact.
She is now accused of actually having sex with the 16-year-old boy.
The district attorney's office said the investigation began when the victim's girlfriend discovered suspicious texts on his phone.
"Rule No. 1 if you are a teacher or a coach, do not have sex with a student," District Attorney Tom Hogan said. "Breaking this rule is a one-way ticket to arrest, losing your job, and prison."
Bonkowski, of Stowe, resigned earlier this month.
Anyone with information is asked to contact investigators at (610)344-6866.