Officials say that Michelle Jacoby, 27, from Riverside, was charged with aggravated sexual assault and endangering the welfare of a child.
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Jacoby was a special education teacher, according to the school's website.
The investigation began after authorities were informed that the student had disclosed his relationship with Jacoby to another teacher.
Investigators revealed that the relationship, which had since ended, involved multiple encounters over a two-year period.
It began when the student was a freshman, officials say, and most encounters took place at Jacoby's home.
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Riverside Superintendent Michael Adams said that Jacoby, who also serves as the Riverside High School marching band director, has been suspended.
"The safety of our students and staff is absolutely paramount," Adams said in a statement to the school community. "Therefore, I want to assure you that based on the information shared with me regarding this specific allegation from a few years ago, there is no current safety concern for our staff or students. The School District will continue to cooperate fully with the authorities regarding this situation and will continue to provide the appropriate support/training for our staff and students."
Jacoby was taken into custody on Tuesday night and released on Wednesday following a court appearance.
The Burlington Township Prosecutor's Office and the Delanco Township Police Department are still investigating the case.