When the Declaratory Act was first brought to the General Assembly in May 1891 a number of opponents of the Act withdrew from various Free Church Congregations on Bute and began meeting in a hall. They asked Rev. A M Bannatyne, who had demitted his charge in Aberdeen, to be their pastor. In 1905 the Free Presbytery of Glasgow appointed a delegation to meet with this group and take the necessary steps to regularise matters and establish the Free Church of Rothesay continuing. On 27th December 1905 Rev. Alex Stirling was inducted. Services ceased in 1997.

At the Reconstitution of the Free Church in 2000 the congregation was vacant. Services were resumed in 2001.