Nicky Morgan took action following the 'Trojan Horse' scandal where a number of schools were accused of pushing an extreme Islamist agenda.
She called on all schools to broaden the horizons of pupils and not close minds.
She also encouraged them to teach respect of other people, even if they don't agree with them.
The guidance has received criticism from some Christian groups.
Speaking on Premier's News Hour last month, Simon Calvert from the Christian Institute raised concerns: "Nobody can accept all faiths.
"Should everybody accept Scientology? Or should we be able to say, 'Actually, we think it's profoundly wrong.'
"That's the problem with this vague, warm and fluffy wording that we're getting from the Department of Education.
"What we need is for them to go back to the drawing board and talk to the faith schools."
But the Church of England's Chief Education Officer has released a statement of support
Revd Nigel Genders said "Church of England schools have always been committed to providing a high quality education for all young people, of all faiths and none.
"Clearly this must include rigorous and challenging religious education to equip young people with the knowledge and understanding of a range of faith systems. We were delighted that the government recently acted to support us in doing this by providing bursaries for those training to teach RE.
"We take just as seriously our role to ensure that the rights of LGBT young people are included in the curriculum and that they feel welcome in our schools. That is why we developed a resource to help all schools combat homophobic bullying. We are delighted that the Secretary of State is now funding a major project on this issue.
"All our schools teach about same sex marriage being the law, but we also feel it is important to reflect that there are different views on marriage, including that of the Church, and we would expect all schools to do the same."