The 14-year-old boy, who received special-education services from the school, reported having sex with his teacher on "several occasions," said police spokeswoman Officer Jillian Russell.
When the boy's father discovered the relationship, a school source said, he pulled the boy from Ethan Allen.
Amato, who was awaiting arraignment Wednesday night, could not be reached for comment, and it wasn't immediately clear whether she had a lawyer.
She has been a teacher for six years.
Amato can be seen on her Facebook page mugging with young men.
"My fav students!!" a picture she posted on Tuesday reads.
"Fun with these kids!" appears with another photo posted on Tuesday. In that photo, she appears to be in a car with several young men, some of whom are extending their middle fingers.
The school source, who asked not to be identified because staff were asked not to talk to reporters, said that Amato would often spend time out of school with groups of her students.
Fernando Gallard, a spokesman for the Philadelphia School District, said that allegations were first made to the school in April.
School officials then notified city and school police, and removed her from the classroom pending an investigation.
She was also barred from having contact with students.
She is currently suspended with pay, Gallard said, but after an administrative hearing next week could lose her pay.
Ethan Allen parents were informed of Amato's arrest through a letter sent home Wednesday.
Principal Cassandra Houston said that the district is "working closely with the Philadelphia Police Department's Special Victims Unit to ensure that a thorough investigation is conducted."
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