The church was founded by Thomas Gillespie, a former minister of the Church of Scotland. He had been deposed by the General Assembly in 1752 after he refused to participate in inducting a minister to the Inverkeithing parish since the parishioners opposed the appointment. Gillespie was joined by Thomas Boston of Oxnam and Thomas Colier of Westmoreland. They held the first meeting of the Presbytery of Relief at Colinsburgh in Fife in 1761.The number of congregations grew rapidly, and a Relief Synod was formed in 1773.
In 1847 118 of the 136 Relief Church congregations went into union with the United Secession Church to form the United Presbyterian Church.