The apology from the church’s bishops came in a report following five years of debate on the church’s position on sexuality.
The report will be delivered to the church’s national assembly, the General Synod, which is meeting in London next month.
“We want to apologize for the ways in which the Church of England has treated LGBTQI+ people — both those who worship in our churches and those who do not,” the bishops said in a statement.
“For the times we have rejected or excluded you, and those you love, we are deeply sorry. The occasions on which you have received a hostile and homophobic response in our churches are shameful, and for this we repent.”
Nonetheless, the Church of England’s stance that matrimony is restricted to unions between one man and one woman will remain in place.
It has proposed offering same-sex couples the chance to have a church service with prayers of dedication, thanksgiving or for God’s blessing after they have a civil wedding or register a civil partnership.
Same-sex marriage has been legal in England and Wales since 2013, but the church did not change its teaching when the law changed.