The headmaster of a prestigious Melbourne private school that controversially sacked its deputy for cutting a student's hair has resigned.

Trinity Grammar said Michael Davies tendered his resignation and will leave at the end of the school term.

The private school in Melbourne's leafy inner-east came under scrutiny when it fired long-serving deputy headmaster Rohan Brown for cutting a student's hair on photo day.

The school council made the decision in March because Mr Brown "contravened disciplinary procedures".

But after a series of protests by students and parents and an independent review, the school offered Mr Brown his job back and he returned to school in April.

Rohan Brown was warmly welcomed by students when he returned to work. ( ABC News )

The campaign to reinstate the deputy headmaster included the use of a truck mounted with LED screens, which circled the school at pick-up time showing messages calling for Dr Davies and the council to resign.

The events also exposed a deepening rift over the direction of the all-boys school.

In a statement, Dr Davies said he made the decision to step down after speaking with his family.

"Having successfully resolved some complex matters over recent weeks, I am now content that our hard work in recent weeks has helped the school return to a position where students and staff are enjoying the normal rhythm of life," he said.

"As a school we have made tremendous strides over the past four years and I have enjoyed my time here immensely."

The chairman of the school council, Robert Utter, said he was sorry to see the headmaster leave after he helped Trinity become one of the best performing schools in the state.

A truck with an anti-Michael Davies billboard was driven outside the school to protest the sacking. ( ABC News )

"Over the past four and a half years Dr Davies has been instrumental in the school's continuing evolution as a leading private education institution," Mr Utter said.

"It would be easy to forget these achievements given recent circumstances at the school but they remain accurate measures of our recent history."

The independent review was led by former Federal Court judge Raymond Finklestein QC and barrister Renee Enbom, who represented Rebel Wilson in the Hollywood star's recent defamation case. It found Mr Brown's dismissal was not justified.

It led to the school reinstating Mr Brown.

On his first day back at school, the deputy headmaster tearfully apologised for the "disruption" caused by the saga but said he was happy to be back.