Methodist Ladies' College in the Melbourne suburb of Kew terminated the employment of Kam Kenny-Jones in September when the allegations first came to light.
Kenny-Jones, 32, taught students in years 7 to 12 at the college, which charges annual fees of up to $46,410.
Victoria Police confirmed a Thornbury man was arrested on Saturday.
"He has been charged with three counts of sexual assault of a child aged 16 or 17 under care, supervisor, or authority," police said in a statement on Tuesday.
The charges relate to a sexual assault on July 2, the statement said.
The man has already appeared before a court and was bailed to appear before Ringwood Magistrates Court on December 2.
It is understood the charges involve one senior student, but the school, which said the news would be "confronting and concerning for our community", is asking families with any concerns relating to the teacher to contact its senior child protection officer.
Kenny-Jones had his position terminated after the school's code of conduct was breached, the school said in a statement.
"In September 2026, the College became aware of serious concerns about Mr Kenny-Jones," the statement said.
"He was immediately stood down that day from his duties while the matter was investigated and reported to the relevant authorities, including Victoria Police."
After being advised of the charge, principal Julia Shea wrote to the school's families on Monday about the matter and outlined supports available to students.
The principal and other senior school leaders have also personally contacted many of the parents of students who had classroom contact with Kenny-Jones.
"Given the nature of the charges, I have made the decision not to communicate this information directly to students," Ms Shea said in a note to parents.
"I believe parents and carers are best placed to decide whether and how to have this conversation with their daughter, so that she can hear this news from you and have your support as she processes it."
In Victoria, anyone who has sex, touches someone sexually or performs a sexual act in front of a child 12 or under can be charged with sexual assault, according to Victoria Legal Aid.
The same applies for children aged between 12 and 15, even if they agree, a person more than two years older can be charged with sexual assault.
It's the same for a person who cares or supervises has sex with someone between 16 and 17 years old, even if they agree.
Police said the assault took place in Mont Albert, a suburb roughly 10 minutes drive from the school.
1800 RESPECT (1800 737 732)
National Sexual Abuse and Redress Support Service 1800 211 028
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