In 1806, a decision was made to build a "Chapel-of-Ease" to serve the growing population of mainly poor people in the southern area of the Parish of Hackney. Called the 'Chapel of St. John of Jerusalem', it was located on the north side of Well Street. The Chapel, a plain building capable of holding 750 people, was consecrated on 13th May 1810.

The Rev. Henry Handley Norris who had been the perpetual curate, and then vicar, erected at his own expense a school  attached to the Chapel. On 15th April 1831, the Parish of St. John of Jerusalem, South Hackney was created and Norris became the first Rector.

Despite enlargement of the Chapel to serve the increasing population, a decision to build a new church was made in May 1842. At this time the parish had a population of 5,790 in 1,042 houses.

By 1844, a scheme designed by E.C. Hakewill had been chosen, the foundation stone being laid 15th May, 1845. The cross was mounted at the top of the spire on 21st February 1848. The building was consecrated on Thursday, 20th July, 1848, by the Bishop of London with a full congregation of over 1500 people, including 200 robed clergymen. The Bishop preached an excellent sermon, during which he mentioned a shortfall of £600 out of the £16,000 the building had cost. The ensuing collection amounted to £617!

In contrast to the Chapel, the new Church possessed considerable grandeur and was built in crucifix form in early English style to bold proportions, the nave measuring 60 feet in height and the spire 187 feet. The chancel had a stone grained ceiling, while the nave had open fir timbers. The Kentish stone forming the walls was faced with either Speldhurst stone dressing or plaster, there being no brick used. All the pews were of oak and a stone scat ran around the chancel. The organ came from the old Church of St Augustine of Hippo at Hackney. Stained glass was used throughout.

The building remains substantially unaltered to the present day with the exception of the glass and stone spire which was damaged by bombs during World Way 2. Repairs were carried out by N. F. Cachemaille-Day, who put a slender copper clad wooden structure, on the tower, giving the now familiar green spire.