Chad Millington, whose 12-year-old son is a pupil at Holy Trinity Academy in Priorslee, Telford, say they have been told they cannot use a bus that stops a short distance from his home because it is only for Catholic, Church of England and other church pupils.
A change in circumstance means that the boy, who already studies in Year 7 at the school, now has to live permanently with his mother in Wellington.
The family have tried to arrange for school transport for him, but were told he cannot use the bus to travel to the multi-faith academy as it is only for church-going pupils.
Mr Millington, who lives in Newport, said: "The bus stops two minutes from the front door. But he was told because he's not Catholic, even though he goes to the school, he can't use it. I know other people are having a similar issue.
"If we use public transport, the nearest bus stop to the school means he will have to cross the busy road which isn't safe. And taxis there and back would cost a fortune."
The 900-place Holy Trinity Academy in Teece Drive, Priorslee, which opened in 2015 was built as a joint venture between the Roman Catholic Diocese of Shrewsbury and the Anglican Diocese of Lichfield.
It replaced the Wellington Catholic school Blessed Robert Johnson.
The purpose-built academy, along with the Charlton School, was the last in Telford & Wrekin Council's £200 million Building Schools for the Future project. Though the school is an academy, the buses themselves are run by Telford & Wrekin Council.
Emily Taylor, a spokeswoman for Telford & Wrekin Council, said that special arrangements were made to Catholic families and that other transport assistance was only offered to children from low-income families, within a certain radius of the school.
She said: "Transport assistance is offered to pupils who are baptised Catholics and pupils whose families are faithful and regular worshippers in a Church of England Parish Church or other Christian affiliated churches if they live over the three-mile distance criteria for secondary aged pupils.
"A pupil from a low-income family will be entitled to help with transport to their three nearest suitable LA schools where they live more than two miles but less than six miles from the school.
"When a parent prefers to send their child to a school which is not their designated nearest school from the home address, the parent will assume responsibility for the provision of transport and associated costs."