The Church of England wants to create a new church-aided school on the site of the former Cowley St John School, in Cricket Road, Cowley, Oxford.
The new Anglican school would admit 1,200 pupils and could be open by September 2003.
The Anglicans made the surprise announcement following the apparent ending of hopes to reach agreement with Catholics over the future of the joint secondary school, St Augustine's, in Iffley Turn.
Since Cowley St John closed in the 1980s, its buildings have been used as offices for the local education authority and adult education.
Transforming them back to a school would cost tens of thousands of pounds, but Anglicans now want a new Church of England-aided school included in the controversial plans to switch Oxford schools from a three-tier to two-tier system.
St Augustine's was for years held up as a symbol of the churches' successful working partnership in local education.
However, they fell out after the Catholics decided to press for their own secondary school in the city, with the abolition of middle schools.
The Bishop of Oxford, the Rt Rev Richard Harries, made clear his disappointment that agreement could not be reached to save the joint school.
Bishop Harries said: "It is with deep pain and regret that we accept that all the efforts to persuade the Catholic Archdiocese of Birmingham to remain a partner at St Augustine's have failed. "
He said the Anglican Diocesan Board, suddenly faced with the loss of its presence in secondary education in the city, had decided to set up a new church school.
Danny Sullivan, director of the Oxford Diocesan Board of Education, said: "It will be both distinctive and inclusive: distinctive because it will be part of the rich Anglican tradition of service in education; inclusive because it will serve its local community alongside the needs of Christians and those of other faiths who seek a Church of England Secondary School."
It would include 1,050 pupils aged 11 to 16, with provision for a sixth-form of 150 pupils.
The Oxford Diocesan Board is to publish a consultation document setting out its plans.
The proposal adds a new twist to the increasingly complicated schools reorganisation, which will now see both Anglicans and Catholics set on creating church schools.
Earlier the independent schools adjudicator was asked to rule on a bewildering list of options.
The governing body of St Augustine's School wanted their school to continue as a joint Catholic/Anglican school.
The favoured Catholic solution was to stop Oxfordshire County Council from closing Cardinal Newman School, also in Cricket Road.
They say that the middle school should be turned into a secondary school to meet "the overwhelming support " for Catholic education in Oxford.
Comments: Our rules
We want our comments to be a lively and valuable part of our community - a place where readers can debate and engage with the most important local issues. The ability to comment on our stories is a privilege, not a right, however, and that privilege may be withdrawn if it is abused or misused.
Please report any comments that break our rules.
Read the rules hereComments are closed on this article