Rev Dr Rob Craig will succeed the current Moderator, the Right Rev Dr Roy Patton, who leaves office in June.
Dr Craig had an overwhelming margin of 17 nominations to two over the other contender, the Rev John Dickinson from Carnmoney on the outskirts of Belfast.
Speaking to the Belfast Telegraph shortly after his election last night, the Moderator-designate said: "I regard this as a vote of support for the Presbyterian churches in this area and also as a recognition of Londonderry as the UK City of Culture. During my year of office, I will try to be a good ambassador for the city wherever my duties may take me."
Rev Craig has been minister of Kilfennan Church in the Waterside area since 1994.
He said: "I have spent longer in Derry than anywhere else in my life. My family and I have been made to feel at home not only by the Presbyterians, but by all the communities in Derry. I look forward to working with other church leaders and I intend to share in joint worship with others in services at Christmas and on other occasions."
He underlined that one of the major themes of the Church is transformation.
"We need to bring the churches out of the buildings and to learn to relate better to the wider community and to meet their needs," he added.
Dr Craig said that last night's vote by Parliament to legislate for same-sex marriage applies only to England and Wales, but that in the longer term it could increase pressure in Northern Ireland for such a measure.
He said: "We need to be vigilant to uphold the traditional Christian teaching on marriage. I do not support same-sex marriage, but in my ministry I have been helping families where the issue of sexual orientation causes suffering and hurt. My role has been to uphold Bible teaching and also to show compassion and understanding."
Asked whether the Presbyterian Church could do more to help bring a solution to the Union flag issue, he said: "I do not take office until June and I am fully supportive of the measures taken by the Moderator and the Church to deal with this issue. I am also supportive of the work being done to try to find a solution, particularly in east Belfast."
The Rev Dr Rob Craig (58) was born in Magherafelt and educated at Queen's University and later at Union Theological College.
He was an assistant minister at Glengormley, and from 1985 he was minister of Clough and Seaforde.
He has been at Kilfennan since 1994. Dr Craig's wife Karen is a primary school teacher, his daughters Rachel (25) is a trainee solicitor and Hannah (23), a nurse.
He is "a late starter" at golf and he supports the Ulster and Ireland rugby teams and Tottenham Hotspur.