Sarah Macdonald's resignation is the latest twist in a saga that has seen Colin Hall, the head, come under fire from parents and teachers for allegedly abandoning the school's progressive traditions.
It followed only days after an inspectors' report had praised Mr Hall's "strong and inspirational leadership". It said that Holland Park was an improving school that had improved faster under him.
But the National Union of Teachers says the treatment of two of its members, who were denied progression up the pay scale under a "flawed" process, was "appalling".
Earlier this year, two long-standing teachers, who are active NUTmembers, were refused progression up the upper pay scale by governors on the personnel committee.
The NUT challenged the decision, arguing that the process for determining progression was seriously flawed and prejudiced against their members.
After a long delay, and a postponement, the decision was overturned by an appeal panel of three governors.
Ms Macdonald, who was not involved in the original decision, is understood to have resigned after the appeal hearing was postponed.
She declined to give the reasons for her resignation to The TES this week, although she said it was "not over any single thing".