The new guidelines he proposes will be entitled 'Valuing All God's Children', and they will be announced from a school in Lewisham in south east London.
In an article written for the i newspaper, Archbishop Welby said: "The aim of this guidance is to protect pupils in church schools from having their self-worth diminished, and their ability to achieve impeded, by being bullied because of their perceived or actual sexual orientation."
He admitted that this would be a difficult area, especially for Christian educational establishments: "Sexuality is a highly sensitive and complex aspect of our humanity, of course, and church schools face particular challenges in this area."
The Archbishop, who voted against same sex marriage in the House of Lords, says one major challenge is "the complexity of combating homophobic bullying while still teaching the traditional Anglican view of marriage, especially in the light of the revolutionary change to its legal definition for the accommodation of same-sex couples".
Archbishop Welby said that this particular challenge needed to be faced "head on".
However he also suggested that his proposal would not involve the imposition of ideas or beliefs upon pupils: "At every church school there will be a wide spectrum of beliefs, and this must be acknowledged and respected."
These kinds of actions are something the Archbishop believes is required of Christians.
"The gospel instructs Christians to love our neighbour as we love ourselves," he said. "That is an instruction, not an optional extra."
The importance of these issues is borne out in the statistics. A recent survey of LGBT individuals aged between 16 and 25 found that 49 per cent said that their time in school had been characterised either by actual or threat of discrimination.
Archbishop Welby notes that because of the number of people being educated in Church of England schools, nearly one million, this issue was not one that he and the Church of England could just "wring our hands over".
The guidelines are not going to be related to specific educational material, but rather will focus on creating a broad anti-bullying environment: "This is not about providing lesson plans or materials for PSHE or sex education. It's about challenging schools to strive towards a deeply accepting environment for all their pupils."
Amongst the plans, there will be included a "zero tolerance" to what the Archbishop calls "the victimisation and diminishment of young people through homophobic language or behaviour".
This kind of practice is, according to the Archbishop, "anathema to Christian practice".
The guidelines aim to help children "respectfully disagree" and base their guiding principles around a metaphor used by Professor Trevor Cooling from the National Institute of Christian Education Research, which describes school as a Bedouin "tent of meeting".
The Archbishop believes that these new guidelines will mean that children "will be helped to develop essential qualities for living in our divided and contentious world, with all its moral and spiritual diversity".
"My hope and prayer is for this new guidance to become a significant tool for helping church schools develop and sustain consistency between our Christian values and the daily experience of pupils in our care," he said.