The congregation of Rothes Free Church, which sat within the Presbytery of Aberlour, was established in 1843 at the time of the Disruption, when the minister and a large proportion of the congregation of Rothes Parish Church adhered to the Free Church. Church and manse were both built in 1843-1844 and a new church was later erected and opened in 1900. Following the union of the United Presbyterian Church and the Free Church of Scotland in 1900, Rothes Free Church became Rothes United Free Church and upon the 1929 union between the United Free Church of Scotland and the Free Church of Scotland, the congregation was renamed Rothes High Church of Scotland. In 1939 Rothes High was united with the congregation of Rothes Parish Church, and after the local union the parish church continued in use as the place of worship, although the former High Church was retained for occasional use as a church hall. In 1982 Rothes Church of Scotland was linked with the congregation of Knockando, Elchies and Archiestown and the linked charge sits under the jurisdiction of the Presbytery of Moray.