The National Secular Society has sent a letter to the council.
Its campaigns director Stephen Evans urged the local authority to amend its policy to ensure that all children are treated equally, irrespective of their faith background.
It comes after a 12-year-old boy, who lived with his father Chad Millington in Newport, was told he could not use a bus because he does not attend church.
The boy, who is a pupil at Holy Trinity Academy, Priorslee, Telford, was told the bus, which stops a short distance from his home, is only for Catholic, Church of England and other church pupils
A change in circumstance means that the boy, who is in year seven at the school, now has to lives permanently with his mother in Wellington.
Mr Evans said: "Faith schools being allowed to discriminate against pupils on religious grounds does not justify a local authority discriminating against non-Christians in a similar fashion when providing school transport.
"Once children have been accepted into a school it's reasonable to expect that any travel assistance they receive from the local authority will be fair, equitable and non-discriminatory.
"Discrimination in school transport provision may be regarded as a side issue compared to the wider issues of discrimination caused by faith schools, but for the families on the receiving end and for the children who can't sit on the same bus as their friends and neighbours, this unfairness is very real."
The National Secular Society works towards a society in which all citizens, regardless of religious belief, or lack of religious belief, can live together fairly and cohesively.
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.