The congregation of what is now the High Church of Stornoway first came together as a congregation of the Free Church of Scotland in c1886 although it has roots going back to the formation of the Free Church formed at the disruption in 1843. In 1900, the Free Church united with the United Presbyterian Church and the Stornoway congregation became the United Free High congregation. Of the United Free Church of Scotland.
A new Free Church Assembly was established by those Free Churches that had declined to join the new union. The new Free Church, who saw themselves as the continuing Free Church took a case to the Court of Session and then the House of Lords. The law Lords ruled in their favour and, as a result, the United Free High Congregation were evicted from their home on Kenneth Street in December 1904. Instead, they met in the Seminary (which likewise was given up in 1907 and the manse in 1906) and the hall of the United Free English Church.

On 1 August 1909, the Church took possession of its new home at the corner of Matheson Road and Goathill Road. In 1929, the congregations of the United Free Church united with the established Church of Scotland, with the Stornoway church becoming the Stornoway High Church of Scotland.