The church was founded in the twelfth century by Benedictine monks, so that local people who lived in the area around the Abbey could worship separately at their own simpler parish church, and historically it was within the hundred of Ossulstone in the county of Middlesex. In 1914, in a preface to Memorials of St. Margaret's Church, Westminster, a former Rector of St Margaret's, Dr Hensley Henson, reported a mediaeval tradition that the church was as old as Westminster Abbey, owing its origins to the same royal saint, and that "The two churches, conventual and parochial, have stood side by side for more than eight centuries — not, of course, the existing fabrics, but older churches of which the existing fabrics are successors on the same site."
St Margaret's was rebuilt from 1486 to 1523, at the instigation of King Henry VII, and the new church, which largely still stands today, was consecrated on 9 April 1523. It has been called "the last church in London decorated in the Catholic tradition before the Reformation", and on each side of a large rood there stood richly painted statues of St Mary and St John, while the building had several internal chapels. In the 1540s, the new church came near to demolition, when Edward Seymour, 1st Duke of Somerset, planned to take it down to provide good-quality materials for Somerset House, his own new palace in the Strand. He was only kept from carrying out his plan by the resistance of armed parishioners.
In 1614, St Margaret's became the parish church of the Palace of Westminster, when the Puritans of the seventeenth century, unhappy with the highly liturgical Abbey, chose to hold their Parliamentary services in a church they found more suitable: a practice that has continued since that time.
By the 1970s, the number of people living nearby was in the hundreds. Ecclesiastical responsibility for the parish was reallocated to neighbouring parishes by the Westminster Abbey and Saint Margaret Westminster Act 1972, and the church was brought under the authority of the Dean and Chapter of Westminster Abbey.
As well as marrying its own parishioners, the church has long been a popular venue for society weddings, as Members of Parliament, peers, and officers of the House of Lords and House of Commons can choose to be married in it. Notable weddings include:
5 July 1631: Edmund Waller and Anne Banks, who was an heiress and a ward of the Court of Aldermen, were married at the church in defiance of orders of the Court and the Privy Council of England. Waller had previously carried the bride off and been forced to return her. On a complaint being made to the Star Chamber, Waller was pardoned by King Charles I.
On Easter day in 1555 a former Benedictine monk, William Flower entered the church and attacked a priest who was administering the sacrament. Although he repented for the injury he caused the priest, Flower would not repent his motive which was based on a rejection of the doctrine of transubstantiation. He was thus sentenced for heresy and burned at the stake outside the church.
During the First World War, Edward Lyttelton, headmaster of Eton, gave a sermon in the church on the theme of "Loving your enemies", promoting the view that any post-war treaty with Germany should be a just one and not vindictive. He had to leave the church after the service by a back door, while a number of demonstrators sang "Rule Britannia" in protest at his attitude.
^From "Memorials of St. Margaret's church, Westminister, comprising the parish registers, 1539-1660, and other churchwardens' accounts, 1460-1603", reported in Notes and Queries (1914), p. 518
^John Richardson, The Annals of London: a Year-by-year Record of a Thousand Years of History (University of California Press, 2000), p. 81
^Wright, A.; Smith, P. (1868). Parliament Past and Present. London: Hutchinson & Co.
^Scott, George Gilbert (1995) . Stamp, Gavin, ed. Personal and Professional Recollections. [London: Sampson Low, Marston, Searle & Rivington] Stamford: Paul Watkins Publishing. ISBN1-871615-26-7.