Deirdre Rowe's departure comes after an investigation into Ampleforth College revealed serious failures by the school to meet child protection standards.
Rowe was appointed as acting head of the north Yorkshire college in August 2018, after spending five years as the college's designated Safeguarding Lead.
The report by the Independent Schools Inspectorate (ISI) raised concerns that bullying and physical abuse were not being properly recorded and concluded that the college's safeguarding policy had not been effectively implemented.
The report inspectors said: "It [the school] does not identify the different responses required for behavioural concerns and safeguarding concerns, particularly with reference to bullying and peer-on-peer abuse and the potential danger stemming from the misuse of internet messaging."
It added: "Incidents involving the physical abuse of pupils are not always recognised as potential bullying or safeguarding concerns."
The ISI's visit was made to check on the progress made by the institution following previous allegations of misconduct.
In 2018, an investigation by The Independent Inquiry into Child Sexual Abuse (IICSA), found a number of historic cases of "appalling sexual abuse" that had stretched over decades.
Ampleforth College said it was looking into all of the issues highlighted in the latest report and that a new interim head will be appointed to bring change and safeguarding expertise to the role.
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