Wendie Schweikert, 36, was charged on Friday with two counts of criminal sexual conduct with a minor after a parent of the boy accused the teacher of having sex with the pupil at school at least twice, Laurens Police Chief Robin Morse said.
Authorities said Schweikert remained jailed on Friday and a bond hearing was set for Saturday. Messages left at Schweikert's home and for the prosecutor were not returned. It was not immediately clear whether she had been assigned a lawyer.
Police said Schweikert, who resigned from her job at E.B. Morse Elementary School on had been an employee of the school district for nine years and had no criminal history or prior complaints against her.
"This is an unfortunate situation that is being taken seriously," district Superintendent Edgar Taylor said in a news release.
"This type of behaviour is not acceptable and will not be tolerated in the district."
Laurens is in northwestern South Carolina.