At a meeting on 8 January 1951, the Down Presbytery banned the elders of the local congregation from using the church hall for a Gospel mission.

[7] In that year, under the leadership of Paisley, four new congregations joined to form the Presbytery of the Free Presbyterian Church of Ulster.

[9] The appointment of Paisley as First Minister of Northern Ireland in May 2007 led to a great deal of controversy within the Free Presbyterian Church.

The church had declared some years previously that it would be unbiblical to have terrorists or ex-terrorists in the government of Northern Ireland.

The church is also strongly opposed to homosexuality, yet the First Minister's office is responsible for protecting LGBT rights in Northern Ireland.

A stormy meeting of the Presbytery of the church in September 2007 resolved the crisis by agreeing that Paisley would step down as Moderator in January 2008.

The church had taken out the 540-word advertisement in the News Letter on 1 August 2008 (one day before the annual Belfast Gay Pride event) calling homosexuality "an abomination"; it "defined homosexuals as perverts and called on religious followers to maintain a very public stance against the gay community".

Fundamentalism has evolved over the years to where the original five essential doctrines that one had to hold to be considered fundamentalist—namely: the inerrancy of the Bible, the literal nature of the Biblical accounts, the Virgin Birth of Christ, the bodily resurrection and physical return of Christ, the substitutionary atonement of Christ on the cross—were mixed with "biblical separatism", a doctrine that advocates avoiding any public or private worship with people of other denominations that it considers apostates or heretics.

At the start of Paisley's ministry this separatism was focused heavily on the Presbyterian Church in Ireland, a denomination from which it drew many of its initial members.

The FPC (on 18 May 2005) published a Book of Church Order in which its governmental policies and procedures are set forth publicly.

[16] The polity of the FPC includes allowing a cleric such as Paisley to hold an apparently indefinite term of office as Moderator.

[18] As of 2004, missionaries were serving in India, Jamaica, Kenya, the Republic of Ireland, Spain, the Philippines and Germany.

These are the Whitefield College of the Bible, formerly based in Banbridge, County Down, but now relocated to Belfast, and the Geneva Reformed Seminary in Greenville, South Carolina, USA.

Free Presbyterian Churches are usually of simple design, following Protestant ideals dating back to the Reformation.