Hathaway resigned prior to surrendering to the authorities.
At the time of the relationship, the student was 17 years old.
She had been with the district since 2012.
In May, the Bedford Police Department became aware of the allegations of a potential inappropriate relationship between 33-year-old school counselor Shannon Hathaway and the ninth grader.
A substitute teacher has been charged with first-degree sexual assault after she allegedly had oral sex with a 17-year-old student on her first day at the job.