St. Francis Anglican Church draws its history, in part, from the Free Anglican Mission Society.

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In 1888 the Nazarene Episcopal Church was founded by the Rev'd James Martin (1843 to 1919) who established his headquarters at Flaxman Road, Loughborough Junction, London, S.E.5. On 11 April 1888 it received episcopal succession when Bishop Alfred Spencer Richardson of the Reformed Episcopal Church of the UK consecrated Dr. Martin. In 1890 Bishop Martin founded Nazarene College to serve as the seminary of his jurisdiction.

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In 1885, while he served as a priest for the Armenian Catholic Church community - a church body in union with the Roman Catholic Church - in Constantinople (from 1881 to 1885), Bishop Leon Checkemian (1848 to 1920) through contacts with Anglicans, converted to Reformed Protestantism and resolved to emigrate to England. Dr. Checkemian had earlier served as an assistant bishop (from 1878 to 1881) for his ethnic group in Malatia (his birthplace), Asia Minor, having received consecration on 23 April 1878 from Armenian Catholic Archbishop Leon Korkorunian (1822 to 1897). As a newcomer he at first found work as a common labourer in order to survive and studied at New College, a Presbyterian seminary.  By 1889 his command of English was such that he obtained employment in Belfast, Ireland through the Presbyterian Church and became a noted lecturer and preacher in the Protestant churches in that city. In order to bring his fellow British Armenian refugees into a non-papal church, Dr. Checkemian established the

United Armenian Catholic Church in the British Isles on 15 August 1889.

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The following year, Dr. Checkemian created the Free Protestant Church of England as a common meeting place for all types of Protestant Christians - Anglicans, Baptists, Presbyterians, Methodists, etc. On 4 May 1890, in order to remove any doubts as to his episcopal status, he received consecration from Bishops Charles Isaac Stevens and Alfred Spencer Richardson.

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Dr. Checkemian came to the attention of the Most Rev'd and the Rt. Honourable Dr. William C. Plunket (1828 to 1897), the fourth Baron Plunket, Archbishop of Dublin and Primate of the Church of Ireland. Archbishop Plunket hated the creeping Anglo-Catholicism within the Anglican Communion which he viewed as a trojan horse for Papal re-establishment over the Church of England. He licensed Dr. Checkemain as a clergyman within the Church of Ireland, where he remained until early 1897,

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In mid-1897, Bishop Checkemian moved to London, where he was in close contact with the above-mentioned independent bishops. They realised that they could be a better witness for evangelical Anglicanism if they could merge their resources together as one church body. On 2 November 1897, the Free Protestant Episcopal Church of England was formed with the union of the Free Protestant Church, the Ancient British Church, and the Nazarene Episcopal Church, with Dr. Checkemian as its first Primus. The FPEC was inaugurated on the above date in St. Stephen's Church, East Ham, London when Dr. Checkemian, Dr. Stevens, and Dr. James Martin first consecrated George W.L. Maeers (for the Spanish Reformed Episcopal Church) and Frederick W. Boucher to the episcopal bench. These five bishops in turn then consecrated Andrew Charles Albert McLaglen (1851 to 1928). The 1878 Constitution and Canons of the Reformed Episcopal Church of the UK was adopted for use in the new FPEC.

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In December 1900 Dr. Checkemian retired as Primus of the FPEC and was succeeded by Dr. Stevens. On 2 February 1917 Dr. Stevens died and Dr. Martin became the third head of the Church. Two years later, on 20 October 1919 Dr. Martin died and was succeeded as Primus by Dr. McLaglen. On 3 December 1920 Dr. Checkemian died.

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A high point of the FPEC was when it obtained recognition by the British Government as a legally constituted denomination. This fact was established in early 1917 when the Venerable Ernest Albert Asquith, Ph.D. (1884 to 1942), 26 Speldhurst Rd., London, the Archdeacon of the Church, was a test case under the Military Service Act of 1916. Clergymen could obtain an exemption from military service under the terms of this Act. The officiating magistrate gave his decision that the Ven. Dr. Asquith was a lawfully ordained minister of a legally constituted Episcopal Church, and therefore a man in Holy Orders within the meaning of the Act. His Worship arrived at this conclusion after investigating the origin of the Orders of the Church and the services used for ordinations and consecrations

which are based on the 1662 Book of Common Prayer.

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While the FPEC started as a reaction against the Anglo Papist and Anglo Catholic movement, many Anglo Catholic elements of liturgical worship have blossomed and become regular in the FPEC and the Free Anglican Mission Society. The Free Anglican Mission Society strives to be a via media between the two liturgical expressions. When we say ALL are welcome, we really mean it!

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In late 2020, Bishop John Bell, Bishop Tim Baker and then Rev Lark J. Muncy of the Free Anglican Mission Society decided to expand the Mission.  Today, Bishop-Elect Lark J. Muncy, appointed by Bishop John Bell, is working to thrust the Mission forward, creating an Independent, and completely affirming and welcoming, community, whilst maintaining traditional worship according to the 1928 Book of Common Prayer.