There first existed a church at Muckairn in the early 13th century. It was built by Harald, the first Bishop of Argyle, and was in ancient years referred to as Cilleasbuig Earaildd (Bishop Harald's Church). In 1618 the parish of Muckairn was united with Ardchattan and, apart from being briefly separated between 1649 and 1664, they remained united until 1846 when Muckairn was disjoined quoad sacra from Ardcahttan. The present day church of Muckairn, which was built in 1829, stands close to the ruins of the 12th century church. After the 1929 union of the Church of Scotland and the United Free Church, Muckairn parish church was united with the former United Free congregation of Muckairn West. Following the union, the Muckairn West church became the church hall and the old parish church remained in use for worship . Muckairn was later linked with Kilchrenan and Dalavich in 1980. The kirk session sat within the presbytery of Lorn until 1963 when, by Act of General Assembly, the Presbytery of Lorn and the Presbytery of Mull were united under the name of the Presbytery of Lorn and Mull.