Rebecca Withrow, 30, of 265 Cambridge Elm Drive in Clayton, is charged with first-degree rape of a child, indecent liberties with a child and sex offense with a student. She is being held in the Johnston County Jail on a $750,000 bond.
Withrow, a former a fifth-grade teacher at Polenta Elementary School, is accused of having sex with one of her students inside her classroom between February and June of 2003.
She resigned from Johnston County Schools last Wednesday as authorities investigated the allegations.
Johnston County Sheriff Steve Bizzell said the boy's mother claims Withrow also had an affair with her husband.
Deputies searched Withrow's former classroom and have seized items that could be used in the trial, Bizzell said, declining to be more specific.
Withrow is divorced and has two young daughters. Her attorney couldn't be reached for comment.