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Chatham Grammar School for Boys will not be admitting girls from September next year.
The Department for Education denied the school, in Letchworth Avenue, permission to become co-educational.
School bosses launched a consultation with parents and pupils in November last year about the move to admit girls. The main reason for the move was a huge under subscription to the school.
Historically it has been the second preference boys’ grammar schools. In 2014, only 55 people made it their first choice, while for 160 it was second behind the Rochester Math School.
The numbers are not sufficient to fill the school, and it means they lose up to £200,000 of government funding per year.
A spokesman for the Thinking Schools Academy Trust, the sponsor of Chatham Grammar School for Boys, said: “The Trust applied for the school to become co-educational because we believe it would serve the needs of all students in the local area, and be in their best interests.”
They said there was a lot of support for the proposal and that the school has made provisions to make sure the number of selective places for boys would not be reduced.
The spokesman added: “We believe that admitting girls to the school remains an exciting proposition that would be of real benefit to young people in our community, and are considering our next steps to support achieving this.”
The school changed its name to Holcombe Grammar School earlier this month, in preparation for the move, and to reflect the name of the old house the school is built around.
The spokesman confirmed the name change would still go ahead as parents and pupils chose the name at the end of the last academic year.
The school will be using the new name more and more over the next year, and by September 2017 all its branding is expected to bear the name.
The spokesman added: “This summer our students achieved another set of outstanding GCSE and A level results, and we look forward to continuing to deliver the highest quality of education to young people in the area over the next 12 months.”
The Department for Education has been contacted for a comment.