The Parish of Clewer St Stephen was formed out of the ancient parish of Clewer in 1872. This was not the first parish to be so formed, for if we go back to the eleventh century when the first buildings were erected on the site of Windsor Castle, we are told that this was done on a hill in the parish of
Clewer. Later the parish of New Windsor was formed, like that of St Stephen some centuries later.
About the middle of the nineteenth century, the district in which St Stephen’s now is, was described as a mere hamlet in which, beside some few respectable cottages, there was a group of as wretched hovels as could be found anywhere in England. Mission work was begun in this district, before the formation of St Stephen’s parish, by the Clewer Clergy and the Sisters of the Community of St John Baptist, (C.S.J.B.) the Clewer Sisters.
In 1866 services began to be held in a house in Clewer Fields. Later St Stephen’s Mission House was built, the foundation stone being laid in July 1867 and the Mission House was blessed by the Rector (Canon Carter) in October 1868. A contemporary account in the Windsor and Eton Express says ‘The Clewer Sisters have been working among the poor of Clewer Fields for many years, but until now they have had nothing but a derelict old cottage in which to gather the children who flocked there to be taught and fed. This new hall, built by public subscription, also has rooms in which the Sisters can sleep and take their meals. Clewer Fields is one of the poorest areas in this town and the good work these Sisters of Mercy do, year in, year out cannot be over emphasized.’
The church was rededicated on 26 May 2016 (Corpus Christi) to both St Stephen and St Agnes by the Bishop of Reading, the Right Reverend Andrew Proud. The Parish was renamed at the same time as Clewer St Stephen with Spital. These changes are in recognition of the creation of the one parish of Clewer St Stephen and St Agnes Spital when the Reverend Andrew Bunch arrived in 1991, and the uniting of the two congregations by the Reverend Ainsley Swift in 2001. The church of St Agnes was built by Canon Carter and opened in 1874. It has now been returned to the 
adjoining Parish of Clewer St Andrew.
Rectors and Vicars
The Reverend George Davenport Nicholas 1873–1917
The Reverend William Edward Boys 1917–1930
The Reverend Albert Ernest Dudley 1930–1933
The Reverend Geoffrey Heald 1933–1944
The Reverend Arthur Digby Sheffield 1944–1956
The Reverend John Anthony Wynne 1957–1965
The Reverend John Nicolson Scott 1965–1989
The Reverend Andrew William Bunch 1991-1997
The Reverend Ainsley Laird Swift 1998–2018 (Rector of Windsor since 2015)
The Reverend Canon Sally Lodge - 2019 to present