The supreme court of the church is the Conference, which is the final authority in the Church in all matters of doctrine, worship, discipline and order.

The first conference in Ireland was called by John Wesley in 1752 and was held in Limerick. With a few exceptions, the Irish Conference had been chaired by the successor of John Wesley, the President of the Methodist Church in England, until recently. In the last number of years the Church has elected a President annually, who chairs the Conference and other committees throughout the year, as well as visiting Methodist congregations all over the island and representing the Church in the public sphere.

Lay and ordained people, both men and women are involved in decision making at all levels. The Methodist Church in Ireland has ordained women since 1978, and women may serve in all positions in the Church. A system of committees deals with a variety of issues within the Church, e.g. Faith and Order, Inter-Church relations, Social Responsibility.