UCL's Institute of Education used a sample of 10,000 people born in the same week in 1970 and assessed whether faith schools made an impact on their results at O-level, A-Level and University.
They found that there were only short-term academic advantages of Catholic schools and Church of England schools, up to O-Level, providing an equivalent of an extra third of an O-Level.
Professor Alice Sullivan, the study's lead author, explained how background was a bigger influence than school: "Pupils who were raised in religious homes were more likely to succeed academically than those from non-religious backgrounds, whether they went to faith schools or not."
The authors say this would explain why religious schools may sometimes do better, as their students are overwhelmingly from religious home lives.
For example, in the C of E schools attended by children in the study, half of the pupils had an Anglican upbringing, 20 per cent were 'other Christian', 9 per cent were Catholic, 3 per cent were of other faiths, leaving 19 per cent having no religious background.
Professor Sullivan added that this should change the perception held by some that faith schools automatically lead to a better education.
She said: "Past studies have claimed an advantage for faith schools, without accounting for the religious background of the pupils. This study suggests that that is a mistake, which may lead to parents over-estimating the advantages of faith schools".
They also accounted for the difference in class, saying students at C of E schools were more likely to be from more advantaged backgrounds but those in Catholic schools were generally less well-off than those who went to non-faith schools.
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