Lauren Loan, of Perkinsville, Co Durham, is a practising Catholic and attends St Leonards RC Comprehensive, eight miles from her home.
But as both of Lauren's parents are Church of England, she has been told she does not meet the criteria for a free pass.
Lauren's mother, Norma, has urged the government to review its policy on free travel to faith schools, claiming her daughter has been made to feel "an outcast".
Lauren attended one of the comprehensive's Catholic feeder schools, St Benet RC Primary in Ouston, after moving from another school.
Shortly after the move, she asked her mother if she could become a Catholic.
Mrs Loan, herself a Protestant, takes her daughter to mass every week.
But the local education authority stipulates that to qualify for free transport to church schools at least one parent must be of the same faith.
Mrs Loan said: "I don't think there are many children who are of a different religion to their parents, but the council classes her as non-Catholic, so she isn't eligible for this pass.
Council decision
"Now she just feels as though she is completely different from everybody else.
"She just feels isolated and a loner."
Mrs Loan said the only way of completing the journey by public transport is to catch two buses, which she does not want her daughter to do on her own.
They hope Durham County Council will decide to grant her a concessionary pass.
A spokesman for Durham County Council said: "There has to be some point where somebody qualifies and somebody else doesn't.
"That's what the admissions criteria is based upon."