It will be the first time a serving moderator has spoken at the Synod.
Rt Revd Dr Angus Morrison will address members about the proposed Columba Declaration - a historic agreement between the two churches.
If agreed the declaration would mean members and clergy will be allowed to worship and minister in each other's churches.
It would also mean churches close to the border could partner up to save money and best use resources.
The proposals are expected to be passed at Synod but will still need to clear the General Assembly of the Church of Scotland in May.
Speaking ahead of his Synod address, Dr Morrison said: "I feel it a real honour to be invited as moderator to address the General Synod. Through the historic Columba Declaration we are proposing to commit ourselves to growing further in communion and to strengthening our partnership in mission.
"By formally recognising the long ecumenical partnership between our churches, I believe we will advance our shared mission of spreading the Christian message of the Gospels."
The declaration has faced criticism from the Scottish Episcopal Church, which already has similar links to the Church of England.
It said it was "deeply hurt" when the proposals were first announced.