St Edmund's College principal Daniel Lawler has resigned, months after his leadership style was publicly questioned and as data shows a significant decline in enrolments.
Mr Lawler will leave St Edmund's at the end of this year and move to South Australia to be with his family.
Parents were told he would continue in education and with his association with the Edmund Rice Foundation.
Mr Lawler wrote to parents on Friday: "I make this decision with mixed feelings, and will miss the most rewarding aspect of being principal of the college, the boys and their great spirit and enthusiasm.
"The last three years have seen the implementation of significant changes and innovation, with the goal of school-wide improvement.
"I believe that these initiatives have and will continue to benefit the education of the students of St Edmund's in the years ahead."
Edmund Rice Education Australia eastern region director Brian Roberts paid tribute to Mr Lawler's work and said the Griffith school would start recruiting for a new leader.
"I congratulate Mr Lawler on his achievements at St Edmund's Canberra and thank him for his contributions to the college community," he said.
School board chairman Michael Cooney thanked Mr Lawler for his service.
"Daniel has been a dedicated school improver and an authentic Catholic leader," he said.
"I'm very grateful for his hard work for our school."
Mr Lawler came under fire in June when a 17-year-old student was suspended after organising a strike on changes to the school's uniform, crest and potentially song.
Multiple sources told The Canberra Times of major concerns about falling student numbers, the departure of long-term staff, changes affecting the identity and pride of the school, the academic achievements of students and a lack of consultation on important decisions.
It is understood half the eight-member board left last year, including two members who were allegedly asked to leave after raising concerns internally and with Edmund Rice Education Australia about the school administration's alleged lack of consultation and decision-making.
Enrolment data revealed a 25 per cent decline in enrolments over the decade, and a 20 per cent decrease between 2010 and 2016.