The special education teacher had sex with her 14-year-old student several times at her home and in her car, the district attorney's office said, according to WPVI-TV.
The encounters, which prosecutors say were consensual, occurred in April and May.
Amato was charged because the boy is a minor.
The counts against her include statutory sexual assault, unlawful contact with a minor, endangering the welfare of a child and indecent exposure.
The boy's father, who was not identified to protect his son, told the station, "I was very upset. She took my kid's youth and I really want justice to take care of this woman," he said.
The dad said his son is "not doing too well. He doesn't want to go to school. He feels humiliated. Since that happened, he (has) changed."
Investigators have seized cell phone records for Amato, and the two also exchanged sexually suggestive text messages, the station reported.
On Tuesday night, before surrendering to authorities, Amato posted Facebook photos showing her hanging out with her students.
She has been placed on administrative leave from the school.