A Catholic boys school in Melbourne's east has agreed to settle a case with a former student after he was allegedly raped by an older student in the school's toilets when he was 12.

Key points: Jonah Pyman alleged he was raped in the Whitefriars College toilets by a Year 12 student when he was in Year 7

Jonah Pyman alleged he was raped in the Whitefriars College toilets by a Year 12 student when he was in Year 7 He is one of two students whose families have told the ABC they were concerned the same Year 12 student was grooming their child

He is one of two students whose families have told the ABC they were concerned the same Year 12 student was grooming their child The school told the ABC it was unable to comment on the allegations

Whitefriars Catholic College for Boys agreed to a confidential settlement with father Trevor Pyman on behalf of his son Jonah.

Jonah sued the school for negligence and alleged he was raped by a Year 12 student in 2013.

The family had argued that the school's negligence led to Jonah suffering psychological injury including post-traumatic stress disorder (PTSD).

Jonah is one of two students whose families have told the ABC they reported concerns to the school that the same Year 12 student was grooming their child.

Whitefriars College declined to answer detailed questions about the incident, including a request for information on whether it had made any changes to its policies on protecting students.

Jonah claimed the assault occurred during production week of the school musical Oliver, when the Year 12 student, Tony*, led him to the school toilets and raped him.

Whitefriars College was established as a Catholic secondary school for boys in 1961. ( ABC News: Gemma Hall )

Advice from mental health professionals suggests the alleged rape and other bullying Jonah experienced at Whitefriars caused him serious psychological damage, leading him to develop borderline personality traits and complex PTSD.

'He would show me things on his phone'

Jonah's mother, Imbi Pyman, said she only learnt about the alleged attack after her son disclosed it to a mental health professional following a suicide attempt in 2015.

"I think he may have used the words at that time that it was consensual, but he says he remembers crying throughout," she said.

The family spoke to police but decided against pressing for criminal charges, fearing a police investigation and prosecution could damage their son's already fragile mental health.

Tony met Jonah during the school musical rehearsals, when it was alleged he talked to him about sex and sexuality, before initiating "physical interactions" with Jonah "backstage, in the toilets, during rehearsal breaks".

"It started with this older student bringing me to the back of the bus … he would show me things on his phone," Jonah said.

"I started to learn about things like pornography. Boys who liked other boys, boys who liked girls and how they're different and what they should do and how they act."

Parents 'immediately' went to school

Outside school hours, Tony — who was at least five years older than Jonah — allegedly groomed him through the online instant messaging app, Kik.

Messages seen by the ABC show Tony sending persistent messages to Jonah, telling him "I f***ing love you" and inviting him out to parties.

Ms Pyman and her husband Trevor found the messages on Jonah's phone in October 2013 and immediately alerted the school.

"When we spoke to the psychologist and said 'there's this other young man and these are the messages', it was quickly brought to our attention that that was classic grooming," Ms Pyman said.

"We immediately went to the school with our concerns … [and were given] a very ordinary response in terms of the grooming behaviour."

The college, in Melbourne's east, allowed Tony to continue studying on campus, under the condition he stayed away from younger students. ( ABC News: Gemma Hall )

The college allowed Tony to continue studying on campus until he finished his Year 12 exams, on the condition that he stayed away from younger students, including Jonah.

Despite this, Tony continued to talk to Jonah and at least one other Year 7 student, both at school and on the Kik messenger app.

Second boy allegedly groomed

That other student, Paul*, told the ABC he was also groomed by Tony after they met during rehearsals for Oliver.

"At the start it was just normal friends stuff," Paul said.

"But [there was] inappropriate behaviour. I remember he would always just be walking past and just like grab your stuff [genitals]."

During the later half of 2013, Paul said he received persistent messages from Tony on Kik.

TONY: Ok one last question... Do you get hard over guys? Do you get hard over girls? I am so proud of you Paul. Like seriously! You are so strong and brave and... I love you <3 Chin up buddy! PAUL: Thanks And I don't over guys But I do over girls :/

When the messages were discovered by Paul's parents, they organised to have a meeting with the school.

TONY: I reckon you don't want coz of your parents (just tell em u r seeing friends from primary school or something) or cos u think im gonna rape you or something idk! You won't tell me why Don't get the wrong impression! Im just saying eastland so we have somewhere to talk face to face coz I don't really want to talk at school or on here

PAUL: I HAVE PLANS THIS WEEKEND!!! Ok?

Paul's mother, who also does not want to be identified, said she was "stunned" when the school told her that Tony would remain on campus.

"Grooming wasn't illegal then, and so the school's reaction in the meeting was that Paul, 13 years old, was a naughty student and shouldn't have been messaging," she said.

Grooming a child under 16 became a criminal offence in Victoria in 2014, after it was recommended by the state's inquiry into institutional handling of child sexual abuse.

Paul's parents considered taking out an intervention order against Tony, but were convinced by the school that they could handle the situation without police involvement.

Paul alleged bullying at the school was detrimental to his mental health. He struggled with depression and anxiety while he was at Whitefriars, at times self-harming and feeling suicidal.

Jonah Pyman's parents, Trevor and Imbi, were worried a police investigation would damage his mental health. ( ABC News: Danielle Bonica )

Ms Pyman said she hoped telling her son Jonah's story would help raise awareness about the risks of grooming at schools and help keep students safe.

"To parents I would say just dig deeper, believe your child," she said.

"It could happen to anybody, basically, and it happened to us."

*Some names have been changed for legal reasons.