The first Presbyterian worship services in Perth and Fremantle were conducted in the early 1850s by Rev Daniel Boyd, but the impetus for the birth of organised Presbyterianism in Western Australia came from Rev David Shearer, who was sent to Perth from the Presbyterian Church in England in 1879.

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In 1886, the Free Church of Scotland sent Rev Robert Hanlin to assist Shearer. On 10 October, 1886, the first service was held at what was to become the Presbyterian congregation in Fremantle, Western Australia.

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Rev Robert Hanlin, conducted the service just two weeks after his arrival from Scotland. He had been appointed by the Colonial Committee of the Free Church of Scotland, initially for 6 months – but he remained until May 1923 – a term of almost 37 years.

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When Hanlin arrived, Fremantle was the second largest town in Western Australia, with a population of around 4500. His first service was in the Oddfellows Hall (no longer in existence) in William Street, where he had to use a packing case as a pulpit. Eleven people attended the morning service, and forty in the evening.

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In 1889, the church services moved to the Fremantle Town Hall to accommodate increased numbers.

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Rev Shearer had obtained land on South Terrace, where a cottage, previously used by the Fremantle Prison warder, was removed. However, the congregation did not have the funds to construct a building, so Hanlin visited the eastern colonies to rally support. This was the start of a long co-operation between the Presbyterian Church in Western Australia, and the church in the larger populated states.

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The Foundation Stone was laid in March 1890, and the church opened in November that same year.​

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Restoration work on the church building was carried out in 1988-89 and 1996. Further restoration work was carried out as the church celebrated 125 years of worship in 2011. The historic pipe organ, still used today, was also restored in 1990.

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A Chinese congregation was part of the Scots family from 1990 – 2004.

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For over 145 years, the ministers, elders, and congregation of Scots have worshipped faithfully together.