The 13 year-old boy says he was inappropriately touched by O'Neill while he was staying over at her house.
According to an arrest affidavit, the investigation began at the end of January when the Goddard Assistant Principle told Midland Police she believed O'Neill and the student were having a relationship.
The boy admitted the relationship to police during an interview.
O'Neill was arrested and later released on a $25,000 bond.
But, during her interview with police she said it happened the other way around, and that she was inappropriately touched by the student.
O'Neill resigned from her job on January 17th before the investigation began.