Paul Davey worked as head of music at the De La Salle School in Croxteth between 1983 and 1989.
He was jailed for 16 months after admitting two counts of indecent assault against the former pupil.
In 1996 the 58-year-old was jailed for two-and-a-half years after abusing four other boys in the late 80s.
The latest victim came forward in 2012 after his mother died, Liverpool Crown Court heard.
The judge, David Aubrey QC, said: "The purpose and principle and mission of the De La Salle order is to touch the hearts of their students and to inspire them.
"You betrayed that, particularly you betrayed your victim."
The court heard how the boy was abused at a retreat while auditioning for parts in school shows in 1987 or 1988.
It was said that the ex Christian Brother told his victim to 'keep your mouth shut' after the abuse had finished.
The judge said the victim had claimed this wasn't the only time he had been abused by someone linked to the Catholic Church.
"He now finds it hard to trust people; teachers and members of the Catholic Church," David Aubrey QC said.
He added: "The abuse had affected his faith...he had been brought up in believing that members of the Church were meant to help and protect him, and that trust had now been broken.
Davey's lawyer, Tom Watson, told the court he was 'very frightened' about going back to prison.