The John Roan headteacher Nadine Powrie has resigned with immediate effect because of ill health.
The news has been announced this afternoon by Greenwich and Woolwich MP Matthew Pennycook, and later confirmed by the school.
Ms Powrie's departure comes after months of turmoil at the Maze Hill school, with several strikes held by teachers over the past few weeks.
Labour MP Mr Pennycook said Carolyn Roberts from the Thomas Tallis school will take over as interim head until the end of term.
He posted on Twitter: "The coming months may be a challenging period for pupils, parents and teachers at @TheJohnRoan but I'm confident in the school's future."
1/3 Change in leadership arrangements at @TheJohnRoan with Nadine Powrie standing down with immediate effect owing to ill health.
— Matthew Pennycook MP (@mtpennycook) May 12, 2016
In a letter to parents, chair of governors Patrick Cooper said Ms Roberts will continue at Thomas Tallis whilst she steps in at the John Roan.
He wrote: "Owing to ill health, Nadine Powrie is standing down as headteacher with immediate effect.
"The governors appreciate how hard Nadine has worked for the school and we are sure that you will join us in wishing her well."
In February this year the school leadership announced plans to restructure to tackle the school's £438,000 deficit.
They blamed its financial crisis on a drop in the number of sixth form pupils joining the school and rising costs.
The school also claimed that Ms Powrie inherited a deficit budget from the previous leadership when she joined in September.
But former headteacher Des Malone spoke out and denied this, saying she inherited a "tight budget" but not a deficit one.
READ MORE: Former John Road head disputes reasons given for school's £438,000 deficit
In a statement he laid out a breakdown of the school's original budget, denying the claim that a loss of sixth form students contibuted to the deficit.
When asked by News Shopper to respond to his claims, they declined to comment.
Last week teachers from the unions GMB, the NUT and NASUWT called off their industrial action after the school announced a U turn on its restructure plans and proposed redundancies.
The proposals could have seen a narrowing in humanities subjects and the loss of 11 teaching positions.
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