In a vote yesterday, a majority of the 171 regional "presbyteries" backed a change to the wording of its constitution to define marriage as "between two people, traditionally a man and a woman".
The word traditionally has been added which means the Church will now accept that same sex people can be in a marriage together.
It is feared the move could cause more disagreements within the Church which is one of the largest American Protestant denominations.
In the past ten years the Church has lost 500,000 followers which some claim is down to its changing stance on gay people.
Since June last year clergy were permitted to perform gay weddings if they wished, but they are not required to do so.
The General Assembly of the Church agreed again "that no teaching elder or session can be forced to conduct a same-sex marriage ceremony if they do not believe it is appropriate".
The change to the wording on marriage will take effect June 21 2015.
Gradye Parsons, stated clerk of the General Assembly, said: "Let us pray that we can allow the Spirit to continue to create in us a common call to follow Christ while respecting each other's convictions."
Gay marriage is legal in 36 American states and the District of Columbia.