Shalom Christian College in Townsville is shutting down its secondary and boarding schools, saying it is in the "best interests of our students".
The north Queensland college was criticised during the Royal Commission into Institutional Responses to Child Sexual Abuse for its handling of the sexual assault of a 14-year-old-girl in 2006.
The commission heard she was assaulted by four boys behind a classroom at the school, when the students were supposed to be in the boarding house.
The Uniting Church, which operates the school, told the royal commission it did not receive enough government funding to keep its students safe.
In announcing the closure, Queensland Synod moderator Reverend David Baker said Shalom would only enrol primary school students next year and its future beyond 2018 was uncertain.
He said the decision had been made for "the welfare and best interests of our students" and that it would allow the school to focus on providing high-quality education.
"We have a responsibility to ensure the school is a safe, supportive and productive learning environment," Reverend Baker said.
"We understand that this decision will be distressing for students, parents, teachers and community leaders.
"We will work with the Department of Education and Training to find places for students throughout Queensland and the Northern Territory, so all students are offered an enrolment for next year."
The royal commission found the college should have done more to support the victim and that there was no system in place to ensure a coordinated approach to responding to sexual assault cases.
Queensland Education Minister Kate Jones said her department was working with the college to help students and staff affected by the decision.
"We'll do everything possible to support students and staff displaced," she said.
"We believe we'll be able to accommodate all students at local state schools and we'll work with families to offer this solution."
"Where possible, we'll also try to accommodate staff looking for work."
The Uniting Church said it would seek to develop a viable long-term operating model for the school before the end of next year.
