Nicky Morgan had 'breached' her duty to 'take care that information or knowledge included in the curriculum is conveyed in a pluralistic manner', Mr Justice Warby said.
The judge allowed the application for judicial review from three families, supported by the British Humanist Association, who claimed Nicky Morgan had taken a "skewed" approach and was failing to reflect in schools the pluralistic nature of the UK.
They were angry at changes to the subject content in the RS GCSE which they claimed gave priority to religious views, in particular Buddhism, Christianity, Catholic Christianity, Hinduism, Islam, Judaism and Sikhism.
The families seeking judicial review included one from Cumbria and one from Kent who cannot be identified.
The third family is Kate Bielby, of Frome, Somerset, and her daughter Daisy.
David Wolfe QC, for the families, told the judge at a recent hearing there was widespread concern "about the Secretary of State's failure to comply with her duty of neutrality and impartiality as between religious and other beliefs".
But lawyers for the Education Secretary, who is a Christian, said neither domestic law nor the European Convention on Human Rights require equal consideration to be given to religious and non-religious views in the curriculum.
They told the judge that provision had been made for schools to study non-religious beliefs and that what was in a school's curriculum is a matter "for local determination" by individual school authorities.
Ruling in favour of the humanists, the judge said: "It is not of itself unlawful to permit an RS GCSE to be created which is wholly devoted to the study of religion."
But when the February 15 2015 decision was made to issue new subject content an assertion was made that such a GCSE "will fulfil the entirety of the state's RE duties".
The judge said that was an assertion likely to be accepted and acted on by schools and their governing authorities.
"The assertion thus represents a breach of the duty to take care that information or knowledge included in the curriculum is conveyed in a pluralistic manner."
As a result, the Education Secretary "has made an error of law in her interpretation of the education statutes".
Earlier this year, the former Archbishop of Canterbury Rowan Williams was among 28 religious leaders who urged the Government to rethink plans to leave out humanism in the new qualification.
A Department for Education (DfE) spokesman said: "Our new RS GCSE ensures pupils understand the diversity of religious beliefs in Great Britain through the study of more than one religion, an important part of our drive to tackle segregation and ensure pupils are properly prepared for life in modern Britain.
"It is also designed to ensure pupils develop knowledge and understanding of both religious and non-religious beliefs.
"Today's judgment does not challenge the content or structure of that new GCSE and the judge has been clear it is in no way unlawful.
"His decision will also not affect the current teaching of the RS GCSE in classrooms.
"We will carefully consider the judgment before deciding on our next steps."