It left her feeling dehumanised and badly affected her mental health.
Ms Courtney, who is transgender, went to teachers to report bullying and was told if she didn't like the school she could leave.
"They were attacks on me because of who I am," she said on Wednesday.
"The people who you're meant to go to, the teachers, shut you down. It was some of the worst years of my life."
Ms Courtney's experience at the school in Tasmania is among testimony included in the report of a parliamentary inquiry into bullying faced by students.
It found bullying, discrimination and harassment were persistent problems in schools across all sectors.
Transgender or gender-diverse students were not always supported in a range of matters including acceptance of name changes and the handling of discrimination or bullying, it said.
A former Catholic school deputy principal told the inquiry he was told he couldn't continue as a leader or teacher because of his marriage breakdown.
The report said Catholic Education Tasmania had discriminated against staff on the basis of sexual orientation and marital status, on the face of it breaching the state anti-discrimination act.
However, Catholic Education Tasmania said it has abided with federal discrimination laws.
Catholic Education Tasmania said it took bullying and discrimination extremely seriously and all schools had related policies and procedures in place.
"We recognise the courage of the witnesses in sharing their experiences with the committee," its executive director Terry McCarthy said in a statement.
"The experiences of children and young people can be difficult and complex."
The organisation would continue to review its educational environments and was confident its employment practices were lawful, Dr McCarthy said.
The inquiry made 33 recommendations, including for more funding for mental health support in schools.
It also called for a state government review of the anti-discrimination act to include a focus on school bullying.
Independent MP Kristie Johnston, who initiated the inquiry, urged the state government to ensure anti-discrimination laws weren't being breached.
Liberal MPs Michael Ferguson and Mark Shelton said some of the inquiry's recommendations went too far and sought to lock-in contested views about sex and gender into law.
"Tasmania doesn't need a culture war over how we protect vulnerable students while respecting freedom of belief," they said in a statement included in the report.
"Faith-based education should not be misrepresented as though religious beliefs ... and student wellbeing are at odds with each other."
The government has been contacted for further comment.
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