Mr Cujes and the Trinity Grammar school council made the announcement ahead of this week's new school term.

The announcement follows Mr Cujes' appearance at the Royal Commission into Institutional Responses to Child Sexual Abuse last year in which he said the school should have done more to investigate claims students were sexually assaulting each other in 2000. The commission has yet to hand down findings from the public hearing.

Mr Cujes' retirement follows the sentencing of former Trinity Grammar teacher Neil Albert Futcher, who learned on Friday he would spend 11 years behind bars for sex crimes against six victims as young as 11.

Mr Cujes started as a student at Trinity Grammar in the 1950s and became a teacher there in 1972. He left in 1979 to work at other schools before returning as headmaster in 1996.

In an address to the school community Mr Cujes said he felt privileged to work at the independent Anglican school.

"After some 41 years of direct association with the school, (my wife and I) both feel it is time to conclude our period of service at Trinity," he wrote.

"The support and encouragement of the extended school community during this time has in the past and continues to be a great joy to us. Similarly, Mrs Cujes and I are mindful of the privilege it has been to lead our school community during these past decades and we are very conscious of God's sustaining and enabling grace throughout this time."

Chairman of the school council Richard Pegg wished Mr Cujes well in an email to families.

"It has been a privilege for past and present members of the school council to work with Mr Cujes in providing a Christian education for our young men consistent with the school's mission," he wrote.

"I have accepted his resignation with regret that his time at the school will be coming to an end but also with gratitude for his leadership of our great school."