The legal case centered on the freedom for schools to advertise some jobs, such as being a head teacher, as only being open to practicing Catholics. Humanists UK argued that EU law means that type of advert amounts to illegal discrimination.
The campaigning group brought legal action against the Catholic Education Service, and wanted to launch a judicial review. But the Rt Hon Lord Justice Flaux has upheld an earlier ruling in the High Court that described Humanists UK's arguments as having a certain artificiality.
Paul Barber, the Director of the Catholic Education Service, describes the legal ruling as "highly significant and extremely welcome".
Speaking to Premier, Mr Barber said recruiting Catholic staff ensures the schools maintain their character.
"There are certain posts for which it's really important that you have somebody who is a full member of the believing community," he said.
More than 850,000 children attend Catholic schools, which Mr Barber says make up 10% of all state schools. They're popular with both Catholic and non-Catholic families.
"In order to provide them with an authentic Catholic education it's essential that we're able to have Catholic staff to lead and teach in those schools," Mr barber continued.
Humanists UK campaign against Faith Schools, and believe it's wrong for education funded from taxes to be provided by Christian denominations. The attempt to launch a judicial review over job adverts is part of that campaign.
Paul Barber says the Catholic Church will continue to defend its role in primary and secondary education vigorously.
"It's not something that can be done lightly or cheaply and we need to have the resources to fight those battles because the alternative is that we lose the rights and freedoms that we've enjoyed for many years."
The Catholic Education Service says the latest court decision isn't open to further appeals, and so Humanists UK will not be able to launch its proposed Judicial Review proceedings.
In a statement, Humanists UK told Premier they believe the case was rejected on a technicality and maintain it's wrong and discriminatory to allow Faith schools to use religious criteria when selecting any staff.
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