Eighty-seven per-cent of the congregation at Westhill Community Church supported walking away from the SEC - the Scottish arm of the global Anglican Communion. Thirteen per-cent opposed the move.
Canon Ian Ferguson said the decision came after "many years" of discussions involving SEC bishops.
He told the Anglican Communion News Service: "Our church was not able to feel they could go on the trajectory that the SEC are going and they wanted to maintain their sense of biblical authority and their fellowship with the wider Anglican Communion which is being torn apart by decisions of some provinces.
"For all of us involved, this has been a very painful time and a very difficult decision to make but we have been put in that position by the decisions of the SEC."
In 2017, Canon Ferguson resigned from the Cathedral Chapter of the Diocese of Aberdeen and Orkney in protest at the appointment of Anne Dyer - a supporter of same-sex marriage - as diocesan bishop.
General Synod, the government body of the SEC, voted in June 2017 to allow same-sex marriage.
Bishop Anne said: "The congregation of Westhill Community Church is a much loved and valued part of our diocese, and I am deeply saddened that they have indicated that they want to pursue potential separation from the Scottish Episcopal Church.
"I will continue to work with Westhill as we begin discussions to enable this potential separation, and will continue to pray for the Rector, Vestry and congregation members in the weeks and months ahead."
Prayers are being asked for Westhill Community Church as they struggle with the hard decision of whether to leave the Scottish Episcopal Church. https://t.co/KCCpJoFs4l— Anglicans in Aberdeen and Orkney (@piskyaberdeen) December 16, 2018
The Primus of Scotland, Bishop Mark Strange, said he had received the news with "great sadness".
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