Two parents who challenged compulsory religious worship in school assembly have won the right for a secular alternative for their children.

A Church of England multi-academy said it would allow the children to withdraw from the assembly and prayers, it was confirmed on Wednesday.

The Oxford Diocesan schools trust said a small number of pupils would be provided with alternative materials overseen by a teacher, instead of having to take part in collective worship.

The trust had been facing a court case over collective worship in one of its schools but has agreed with Lee and Lizanne Harris that their children – who attend Burford primary school, in Oxfordshire – had to be provided with a prayer-free, secular class, away from the usual assembly.

Humanists UK, which backed the Harris family, said the decision marked a “significant win” in ensuring that schools did not force religious worship on children.

The Harrises launched the case after discovering their children were being made to pray and watch re-enactments of Bible scenes, including the crucifixion, during assemblies at Burford, an academy with no religious character.

The couple later withdrew their children from assemblies but no alternative activities were arranged by the school. In their submission to the high court in London, the parents argued that Christian worship at the school constituted indoctrination and was in breach of their right to freedom of belief under the Human Rights Act 1998 and the European convention on human rights.

The school’s trust agreed to meet all of the parents’ requests, including providing an inclusive alternative to assembly run by a teacher for all pupils who had withdrawn. It must now inform parents that an alternative is on offer. Religious observance and referring to “god as truth” will be able to take place only in designated collective worship sessions.

The Harrises said: “We are delighted that the school has backed down and agreed to provide our children with an alternative, inclusive, assembly of equal educational worth.

“Ultimately, we took this case to ensure our children receive an inclusive education without the indoctrination of one enforced religion. We believe this isn’t just the right of our children, but all children. The defendant’s reluctance to take this to court in our view shows the growing fragility of this outdated law and those who choose to enforce it.

“This case is hugely significant as it has established that schools have a duty to make inclusive assemblies available to all pupils who want them.”

Humanists UK has drawn up a ground-breaking model that takes religion out of daily school assemblies and focuses on respect for the individual, the environment and justice for the developing world. The campaign group for secularism and non-religious belief said its 200 inclusive assemblies would cover 30 diverse themes in key stages 1 to 5.

Andrew Copson, chief executive of Humanists UK, said: “The 75-year-old English law requiring daily religious worship is so antiquated that it has collapsed in the face of its first legal challenge, without the case being seen through to court. Parliament should now act to replace it with a new requirement for inclusive assemblies in keeping with the nature of our plural society, and government should take a lead in that.”

Anne Dellar, CEO of Oxford Diocesan schools trust, denied the school was organising alternative assemblies for the children concerned. She said: “Burford primary is not offering an alternative assembly – rather, a small number of children who are withdrawn from collective worship will be able to access alternative materials, overseen by a teacher.

“Burford is a happy, successful and inclusive school. While recognising every parent’s right to withdraw their child from collective worship, we are saddened that this case has diverted valuable funds and staff time.”

The Department for Education stressed that the settlement was only between the parents and this school, and that it had no implications for schools across England.