Virtually every member of the General Assembly, which has more than 730 commissioners, expressed support for the UK choosing to stay in the bloc when polls open in a referendum on June 23rd.
The vote took place during this year's annual meeting of the Kirk in Edinburgh and represents the fifth time in the last 20 years the Assembly has formally supported the UK's EU membership.
Member of the European Parliament (MEP) for UKIP and Christian, Jonathan Arnott, told Premier it is not the role of the Church of Scotland to tell people how they should vote.
The politician, who supported a UK exit from the EU, said: "The role of a church should always be, within the community, helping local people.
"It should be doing all the things that Church should do but it shouldn't be telling people how they should or shouldn't vote on a particular political issue.
"Nobody can claim that God is on the side of Remain or on the side of Leave and that's, therefore, something a church should not be making pronouncements on."
In a statement, the Church of Scotland said it was important the Church to "consider its existing stance within the current context of the referendum debate."
Rev Sally Foster Fulton Convener of the Church of Scotland's Church and Society Council, said: "Since 1996 The General Assembly of the Church of Scotland has consistently affirmed the UK's membership of the European Union highlighting the work of the European Union in promoting peace, security and reconciliation amongst European nations.
"Within the Church there are a range of opinions and voices speaking out on this issue. It is important that each individual is able to reflect and come to their own decision on this issue and vote accordingly.
"It is also important for the Church as a whole to consider its existing stance within the current context of the referendum debate. This is what the Assembly were asked to do yesterday and the Assembly chose to re-affirm the long-standing belief that the UK should remain part of the EU."​
Dr Adrian Hilton from Christians for Britain, a group campaigning for the UK to leave the EU, said: "Churches are and ought to be free to comment on any matter of public policy, not least because politics concerns the whole of life in community, and Christians are encouraged to speak out on matters of truth, justice and peace, nudging democratic politicians toward more righteous government.
"But it is interesting that the Church of Scotland was officially "neutral" in the Scottish independence referendum, and is officially pro-Remain in the EU referendum.
"By taking this partisan stance, the CoS leadership risks alienating a substantial proportion of its members over a matter of worldly wisdom.
He went on to say: "The EEC may have been a project for peace, security and reconciliation, but the EU has become a millstone of rancour, division and civil unrest.
"Not all of our neighbours feel embraced by its solidarity and fraternity: look at Greece. The EU is not Europe; Europe is not Christendom; and the Church of Scotland is not its General Assembly but its ordinary members.
"I would encourage all Christians to examine the political facts in the light of scripture, rather than be swayed by the foot-stamping ministers and elders on the Mound."