The children at St Andrew's primary in Keighley, West Yorkshire, are following new guidelines issued by the Bradford diocesan board of education, intended to update the way collective worship is carried out in local C of E schools.
Under the guidelines, separate worship is available to all faith groups, including Christians. Rachel Barker, diocesan education adviser, said: "It's an opportunity for schools to provide overtly Christian worship in a church school which is in addition to the whole school worship."
St Andrew's is one of half a dozen C of E schools in Bradford which have a majority of Muslim pupils. Several other metropolitan areas, including Blackburn and Leicester, have schools in a similar situation.
Under the 1988 Education Reform Act, all schools are required to hold a daily act of worship, thoughonly of a broadly Christian nature.
The controversial legislation has led to children from other minority faiths in some parts of the country being withdrawn from collective worship.
The decision to offer Christian children at St Andrew's separate worship is an attempt to recognise the need to support their faith in a school where it has become a minority.
The new guidelines from the Bradford diocese are issued as the Church of England nationally reviews the future of church schools for the first time in 30 years .
It is expected that the Church Schools Review Group, chaired by Lord Dearing, who is due to visit St Andrew's today, will recommend broadening the Chrurch's admissions policy.
"We need to have a core of Christian children and certainly a core of Christian teachers but we also need to open the gates to others in society," said Colin Hopkins, review group secretary.
A consultation report will be published in December and a final report will follow next summer.