'Flourishing for All' is a set of guidance documents being published ahead of the new school year in September.
The guidance is to be used across the Church of England's 4,700 schools following a consultation running until the end of July.
It replaces the contentious 'Valuing All God's Children', which has been in use in CofE schools since 2014.
The first document in 'Flourishing for All', 'Guidance for preventing and tackling homophobic, biphobic and transphobic bullying', was published earlier this month.
The new guidance has been published to combat "homophobic, biphobic and transphobic (HBT) bullying" in schools.
It advises teachers to use "up-to-date" language on sexuality, sex and gender, and says they must "challenge" the use of "outdated terms which no longer have a place in our vocabulary".
The document then refers schools to a glossary of "up-to-date" terms, including transgender, which it defines as "an umbrella term to describe people whose gender identity is not the same as, or does not sit comfortably with, the sex they were assigned at birth".
Gender is described as "the cultural constructions associated with being male/female or other gender categories, as distinguished from biological sex".
Pronouns are explained as "the words we use to refer to people's gender in conversation – for example, 'he' or 'she'".
"Some people may prefer others to refer to them in gender-neutral language and use pronouns such as they/their," the document reads.
Gender identity is "a sense a person may have of their own gender, whether male, female or another category, such as non-binary".
Writing in the introduction to the guidance, the Bishop of Portsmouth, Jonathan Frost, said: "Bullying has no place in our schools; every child deserves to learn in an environment where they are loved, supported, and respected.
"Our hope and prayer is that these resources will be used by schools across the country to enable such flourishing and ensure that each and every child, knowing they are unique and made in the image of God, will find in our schools a safe environment where bullying of any kind is not tolerated."
The Church of England's Chief Education Officer, Nigel Genders, added: "We are starting with anti-HBT bullying guidance because there is a need in schools for updated guidance this autumn following the Government consultation and the publication of the Cass review.
"We hope these new resources will help to support anti-bullying efforts in schools, ensuring dignity and fairness for all children, which reflects the Church of England's vision for education."
Responding to the guidance, Lucy Marsh of the Family Education Trust said, "It is extremely concerning that the Church of England does not recognise that biological sex is immutable.
"Sex is not 'assigned at birth,' it is determined at conception and recorded at birth. These are biological, unchangeable facts."
Christian Concern said that the Church of England "continues to remain in thrall to gender ideology" and that the new guidance "risks genuine Christian faith being wrongly branded as bullying".
It is urging concerned parents to take part in the consultation before the deadline on 31 July.
"The document is infused with the belief that a gender identity is real," the organisation said.
"This is a false and harmful belief that faithful Christians should not endorse. It is also out of step with the Government's draft guidance on gender questioning children, which refers to this specific worldview as a highly contested ideology and warns of its effects in relation to social transitioning."
A Church of England spokeperson said the guidance had been "informed by reputable existing sources, including Government Guidance, the Cass Review and the Church of England's theologically informed Living in Love and Faith process".