There has been a site of Christian worship on the site of the "old" parish church since at least 1086 - and probably even before then. The first recorded Rector was appointed in 1314 to a Church which included a chapel dedicated to St Thomas Becket and a rood known to have been in a poor state of repair by the fifteenth century.

Sir William Patten, Lord of the Manor, built the present "Old" Church, bordering Clissold Park on the north side of Church Street, in 1563. It is the only church of the Elizabethan period left in London, and one of only a few in the entire country. It is also one of the very earliest Anglican Churches which has never been a Roman Catholic Church.

There have been many additions to the building, notably the Victorian box pews and the spire, placed on top of the ancient square tower by the notable architect Sir Charles Barry.

By the middle of the nineteenth century Stoke Newington had emerged from rural obscurity. The area was being developed rapidly, and in 1849 a new parish of St. Matthias was carved out of the southern portion of St. Mary's, the present church of St. Matthias being completed in 1853. A further division of the ancient parish was made in 1876 with the foundation of St. Andrew's in Bethune Road.

St Mary's was also put on the map by its then Rector, Rev. Thomas Jackson. His sermons attracted huge congregations, too large for what was still a typical village church. But the Rector's generosity resolved the problem: he offered the northern part of the site of the rectory and garden for a New Church.

The Old Church suffered extensive damage during the Second World War but was later restored and is now used regularly for worship and for concerts, such as the renowned Stoke Newington Early Music Festival.