Australian National University School of Music head Peter Tregear will leave the institution at the end of August, three months after the university was embarrassed by the publication of a job ad that appeared to seek his replacement.
The university will now undertake an international search to find a new school head.
The unauthorised job advertisement, published in May, was for a role in addition to Professor Tregear's, whose new contract was due to expire in February, 2017.
Professor Tregear took on the troubled school in 2012 for an initial 18-month contract, which was renewed for three years.
At the time of the advertising stuff-up, deputy vice-chancellor (academic) Marnie Hughes-Warrington said there were no plans to remove the school's existing head, citing "ongoing stability in the school's leadership".
"In addition, the university has agreed to increase the school's funding to allow for the appointment of a second level E academic position to focus on outstanding research and teaching – in addition to the head of school," she said at the time.
The university announced Professor Tregear's resignation on Monday.
He was confident he was leaving the School of Music in a strong position.
"I leave this school with the highest admiration for the commitment and passion of the students and staff to the artform of music and its transformatory potential in the wider community," he said.
"I have done the best I can to take a very difficult situation in 2012 and turn it around, leaving the ANU absolutely convinced that both the university and the ACT need and deserve a school of the highest ambition and quality."
ANU Vice-Chancellor Professor Ian Young said Professor Tregear had played a major role in Canberra's cultural life.
"He has worked tirelessly to build on the School of Music's vision, to promote creative life on campus and in the Canberra community, while attracting Australia's most gifted students to ANU," he said.
As head of the school, Tregear re-established major orchestral, jazz and choral ensembles, ran the Winter Jazz Festival in 2014, directed the digital staging of the opera L'Orfeo and ran the second Australian International Chopin Piano Competition.
He has also overseen major refurbishments including a $1 million renovation of the school's foyer and worked to secure donations.
Last year he appeared on stage with the Rolling Stones. He also helped bring INXS band member Andrew Farriss to ANU as a Coombs Fellow.