Most Revd Justin Welby will address the landmark partnership between the two Church's which was announced last year.
Under the Columba Declaration both denominations would welcome one another's members into congregations and ordained ministers would be allowed to exercise ministry within the existing discipline of each church.
Archbishop Justin's appearance at the Assembly follows a similar move by the Moderator of the General Assembly of the Church of Scotland the Rt Revd Dr Angus Morrison who in February took part in a debate on the Columba Declaration at the General Synod in London, which formally approved the agreement.
Speaking about Wednesday's debate, Dr Morrison said: "We all look forward to welcoming the Archbishop of Canterbury to the General Assembly on Wednesday to speak to the historic Columba Declaration.
"It was my privilege to address the General Synod of the Church of England on the same document and by a very large majority the Synod affirmed it.
"I am confident that our General Assembly will do so too.
"In itself the Declaration is largely of a symbolic nature but it does pave the way for our further growth in fellowship and for extending partnership in mission as sister and national churches who share many common roots, challenges and opportunities.
"We wish this to happen in the closest possible fellowship with other sister churches in the United Kingdom as we seek together to address the challenges of mission in our country today."
The meeting in Edinburgh is set to last six days.
Those taking part will vote on Saturday whether to amend church law to recognise Ministers and Deacons in same sex marriages.
Last year they voted to recognise Ministers and Deacons in same sex civil partnerships following years of debate.