Rev Peter Galloway, the chair of governors at St Olave's Grammar School, has resigned from his role after it was uncovered that the school told 16 students they could not return to the second year of A-Levels unless they got three Bs in their internal exams in the first year of sixth form.
A spokeswoman from the Diocese of Rochester said his leaving "was not because of this situation but it has made him more aware of how demanding the role is and the fact that he does not have the capacity, time and energy to devote to it".
The school was challenged legally in January and made to stop trying to exclude pupils who weren't getting the highest grades. They are one of several high-achieving schools found to be subtly trying to remove those who may let their reputation down.
Lawyers claimed the pupils were initially barred from the school after failing to achieve B grades in exams during their first year of sixth form.
The Department of Education said it has written to many schools telling them they cannot expel certain students based on their ability.
The prestigious Church of England school reversed its decision to exclude the two pupils. Following the U-turn, the students were allowed to return to St Olave's for their second year of sixth form.
Another school who have abandoned the practise is Fortismere School in Muswell Hill - previously run by the current head of St Olave's, Aydin Önaç.
On Monday, the staff association at St Olave's had a meeting in which a several concerns were raised for the headmaster.