Greenwich Council's cabinet last night voted unanimously to close down Blackheath Bluecoat school despite overwhelming opposition from staff and pupils.
The school has failed to reverse a decline in pupil numbers in recent years, in spite of improving exam results.
It will close its doors for the final time in August 2014, with some year groups leaving in 2013.
Council leader Chris Roberts blamed the school's troubled reputation for their decision, saying that "popular mythology" about pupil behaviour was keeping new admissions away.
He also said that the increasing financial deficit racked up by the school, could not be maintained:
"The question is, could the school sustain the improvements it has made with the level of cuts that would be necessary? My view is that it could not."
Decreasing numbers of pupils have not been matched by cuts in staff numbers, leading to the school accumulating a £1.5 million deficit.
Cllr Jackie Smith, the cabinet member with responsibility for schools, said it was unfair for this deficit to continue to impact on other schools in the area.
But in a passionate speech, executive headteacher Jeffrey Risbridger defended his decision to maintain staff numbers, pointing out that results had improved at double the rate of other schools in the borough:
"There has been funding coming to the school that was in excess of funding that we would otherwise have received. But all that has done is allowed us to build confidence and to appoint exceptionally talented, hard-working committed staff who have delivered the goods in the classroom and improved the life chances of pupils as a result. Yes that has costs but was it worth it? You bet your life it was."
He also attacked the council for ignoring the results of their own consultation, which found 91% of respondents opposed to closing the school:
"It could not be clearer that there is no community will in this borough to close Blackheath Bluecoat School. To continue with the closure despite of this is therefore perverse and undemocratic."
He urged councillors to give him more time to turn around the school, and said that the three year window afforded to him by the council had not been a "realistic" period in which to reverse its decline.
The council’s decision means that Greenwich borough will no longer have a Church of England secondary school. CofE schools in neighbouring boroughs are currently oversubscribed.
Chris Roberts admitted that this situation was "not sustainable" and floated the possibility of a new CofE school to be built on the Greenwich peninsula.
However, officers said that there was "no funding stream" currently available for such a school.
Around a hundred pupils and staff marched on the town hall last night to protest against the expected closure of the school and there were chants of “shame on you” as councillors left the building.
Speaking to Greenwich.co.uk after the meeting, executive headteacher Jeffrey Risbridger said:
"I'm shocked and disappointed because it seems clear that the cabinet members didn't listen to any of the points that were put forward either in the consultation or in what was said this evening and have made a decision that is not right for the pupils in the school and for the future of Church of England education in the borough. I accept that these are constrained financial times but I think that children's education is more important than short term financial loss."
He conceded that the council's decision to close the school was "unlikely" to be reversed but said that they were "considering our options."
He also congratulated staff and pupils on a hard fought campaign:
"I think they've done superbly and I'm proud of the very mature, controlled and sensible way in which they've handled themselves. I want the pupils and staff to continue to work as hard as they have to achieve the very best public examination outcomes that they possibly can do, not only for themselves but to demonstrate to the council just how wrong they were to close the school."