The 500 Muslim pupils at Birchfield School in Aston, North Birmingham, can attend lessons taught either by their class teacher or by an Islamic scholar on the staff.
Earlier this year, the parents of 1,500 Muslim pupils in Batley, West Yorkshire, withdrew their children from the official RE programme because they said it was not sufficiently Islamic.
Muslim parents in both towns believe that official RE programmes encourage an overly academic view and are inappropriate for primary pupils.
They have caused alarm among RE professionals, however, who believe the subject will disappear if it is seen as a means of inculcating faith. "If too many people opt out of the official syllabuses, RE will be lost to schools altogether," said Stephen Orchard, of the Professional Council for Religious Education.
"Religious education should not be about making pupils members of faith groups. That is divisive. The point is to help children understand people from other religions as well as their own."
But Mohamed Mukadam, a parent governor at Birchfield, where 70 per cent of the pupils are Muslim, said: "We found the children getting confused because they were being told one thing at home and another at school.
"What we have done here makes sense and accomplishes what the Government wanted in improving moral and spiritual development. Whatever your faith, you have a right to get it across to your child."
"If you want your child to know about other faiths, that can happen in secondary school."
The new religious education course at Birchfield is being taught by an Islamic scholar and teacher training graduate from the City's West Hill College, which runs a specialist Muslim course. It has the approval of both the education authority and the local Standing Advisory Council for Religious Education.
The point of difference, according to Mr Mukadam, a college lecturer, is that the children will learn that Islam is the true faith. Nonetheless, the school says, it will meet legal requirements. Head Andrew Saunders said: "RE takes place on joint themes for all religions within the school. There is a common plan, delivering a multi-faith element."
The children's class teachers will continue to teach RE as before, an option some Muslim parents have taken. Mr Mukadam said that, while the law is flexible in theory, in practice it often encourages "a spectator view of faith".
There is confusion about whether the Birchfield parents have formally withdrawn from official lessons. Mr Mukadam says they have done so, as is their legal right. Birmingham education authority says that they have not withdrawn, and that Birchfield must continue to follow legal requirements.