Stephen and Breege Quinn met Kathryn Stone in Belfast on Thursday.
Paul Quinn was 21 when he was murdered. No-one has been charged.
His family said he had been involved in a dispute with individual IRA members. His mother said the family were being kept up-to-date with the investigation.
She said the commissioner had been very sympathetic towards them.
"She could not believe when she read up on him, the lies that were told about Paul," his mother said.
"She said she will be there to help us. There will be no end till we get justice.
"Every day there's something new comes in and the gardaÃ­ are very, very good.
"They will keep going and we'll keep fighting."
Mr Quinn's family claimed he had been "ordered to leave the country" but refused to do so.
Sinn FÃ©in has denied republican involvement.
After the meeting, Ms Stone said it was a privilege to meet the Quinns and to "witness their strength and tenacity in the pursuit of justice".
"The commission fully supports their search for justice," she said.
"It is my role to advocate for all victims and survivors, and I hope that this meeting with the Quinn family and representatives of the Quinn Support Group, will go some way in reassuring them that they are not being ignored and that the commission is here to help them in any way it can."
Nearly three weeks ago, the Police Service of Northern Ireland released a man in his 20s and Irish police released three other men who were all being questioned about the killing.
The parents of Paul Quinn, who was beaten to death in County Monaghan almost six years ago, have met the Northern Ireland commissioner for victims and survivors.