Brigid Heywood resigned as University of New England vice chancellor late on Friday.
Her resignation came after she was charged with assault earlier this week, following an alleged incident in March this year.
Professor Heywood has been accused of assaulting a teenager at an International Women's Day event in Armidale. It's an allegation she denies.
UNE's Deputy Vice-Chancellor, Professor Simon Evans, will immediate step in as Acting Vice-Chancellor while the University Council, the governing body that the vice-chancellor reports to, begins the task of finding its next VC.
Professor Heywood was the UNE's 14th vice-chancellor.
In a statement on Friday, UNE Chancellor James Harris announced her resignation.
"The University Council and Professor Heywood acknowledge the criminal charges laid against her on 1 August 2022, and the widespread attention and concern this has garnered within the university and the broader community," Mr Harris said.
"In this context, Professor Heywood formed the view that it was in the best interests of the university that she resign from her position, and University Council has accepted her decision."
He said Professor Heywood strenuously denied there was any truth to the charges and will defend them.
"However, both Professor Heywood and the University Council acknowledges the deep hurt felt by many on hearing of the charges and thanks the community for the patience shown as we worked through these matters.
"The University Council wants to clearly state that it remains deeply committed to fostering a safe, inclusive and respectful environment for its students, staff and community at all times."
On Wednesday, Northern Tablelands MP Adam Marshall released a statement detailing his concerns.
He called for the vice-chancellor to be stood aside, pending the outcome of the court case.
The National Tertiary Education Union also weighed in on Thursday, calling on UNE to act.
The acting vice chancellor, Professor Evans, was described by Mr Harris as an experienced university leader with a broad experience base, who he said was well placed to guide the university in the coming months.
Prior to joining the University in January 2022, he was Provost of the College of Arts, Social Sciences and Commerce at La Trobe University, Melbourne, leading academic culture, strategy and performance across the College and its four Schools.
From 2010 to 2018, he served as Pro Vice-Chancellor (International) at the University of Melbourne. Earlier roles in the University of Melbourne's Law School include Deputy Dean, Director of Teaching and Director of the Centre for Comparative Constitutional Studies.
Professor Michael Wilmore will serve as acting Deputy Vice-Chancellor.
"These appointments give much needed certainty to the University community and support the university's smooth continuity of operation at this difficult time," Mr Harris said.
Professor Heywood is due to appear in Armidale court next month.
Make sure you are signed up for our breaking news and regular newsletters
Sign up for our newsletter to stay up to date.