Ronald C. Giglio, 48, of Cedar Lake, Indiana appeared in court Thursday on the charge.
He was ordered to remain in custody, pending a Friday hearing.
Cook County charges were filed on June 28, and he was arrested in Lake County, Indiana before being extradited to Illinois.
A civil lawsuit was filed against Giglio in May by a former student, who accused him of grooming and sexually assaulting her in the early 2000s.
"It really started my sophomore year," the student said.
She has chosen to remain a "Jane Doe," as she filed the civil lawsuit against the teacher, the school and District 206.
Speaking exclusively to ABC7, the alleged victim said the relationship began to escalate her junior year.
"He took interest in my life and my family, my hobbies, it just seemed like he cared," she said.
[Ads /]
She said the teacher was her first sexual experience. The alleged abuse took place off and on campus throughout her years in high school.
At the time, the former Bloom Trail High School student was too scared to speak up.
"It was very clear to me that if I spoke up, his life would be over. He would go to jail. Like, he would lose everything. So, I was scared," she said.
In addition, she said the teacher convinced her she was a willing participant and not a victim. She said their relationship was common knowledge throughout the school.
"We believe, various people, various adults, staff members within the school, who knew that there was something inappropriate going on throughout those years and never, never put a stop to it," her attorney Matt Passen said.
[Ads /]
Passen hopes the lawsuit will finally put a stop to it. He has already heard from a number of others telling similar stories about the teacher, who is also a coach.
While the school cannot discuss legal and personnel matters, in a letter to parents, Bloom Trail Principal Glynis Keene said, "What we can share is that the safety of our students is our number one priority and the listed staff member has been placed administrative leave while the District conducts a thorough investigation."
Jane Doe hopes her lawsuit will encourage other victims to speak out.
"They shouldn't feel shame; the only people who should feel shame are the adults," she said.
The victim also reported the alleged abuse to the police. She said it took her years to come forward after therapy made her realize she was a victim.
The civil lawsuit is back in court Sept. 9.
The video in the player above is from an earlier report.