Nicholas Sampson resigned on Friday, the ABC reported, following the airing by the broadcaster of claims against the school by former female teachers and staff.
The headmaster reportedly resigned following revelations he kept a male teacher on staff who had sent sexually explicit emails to a former female student.
"The School Council ... this morning received his resignation," Cranbrook's council said in a statement regarding Mr Sampson, according to the ABC.
Cranbrook School did not immediately respond to an AAP request for confirmation of the resignation.
The ABC's Four Corners program earlier this week detailed allegations of workplace bullying and abuse at the eastern suburbs school.
The controversy comes as the school, single sex since it opened in 1918, gears up to admit girls from 2026.
In the wake of the claims, former tennis star Jelena Dokic reportedly back out of an appearance at the school ahead of International Women's Day.
On Cranbrook's website, Mr Sampson says the school builds academic curiosity and optimisim in "each of our students, allowing them to thrive in the 21st Century".
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