This beautiful church, on a 1.5 acre site, was established in its present form in 1640 and stands on a hill, overlooking Strangford Lough, the town and Killyleagh Castle. The original building would have been a barn-like structure. King James had awarded James Hamilton land from Killyleagh to Bangor and the church was built on some of this land at the top of Church Hill.
A new spire was added around 1825, paid for by Lord Dufferin. There are records of the church being closed for four months in 1859 as open pews had been installed. Gas lighting was installed by John Martin of Shrigley in 1866. He came to Killyleagh from Pott Shrigley in Cheshire and created a respected model village for his mill workers in Shrigley, about a mile from Killyleagh.
There are a number of plaques and two stained glass windows in memory of various Martin family members. In 1875, a new bell was presented by Catherine Ann Hamilton of Killyleagh Castle. In 1877, the church was enlarged with the addition of a side aisle and new chancel. A new East window was added, along with other stained glass windows, a new Walker organ and choir stalls. The roof was raised and a heating system installed.
In 1940, the Tercentenary year, the Holy Table and Communion linen; choir stalls and prayer desks; a chair and prayer desk for the South side of the sanctuary; a chair and prayer desk for the North side of the sanctuary and a Pulpit desk and Fall were added, gifted by parishioners, family and friends. The font came from the old church at Killowen and is thought to pre-date it. It is made of red porphyry, a hard crystalline rock, deep red and quarried in ancient Egypt. There are also some magnificent stained glass windows. The capstone, placed beside the font, shows the date the church was built-1640.
Over the past 10 years the fabric of the Church has been improved, including repairing stone mullions around the windows and new heating. Currently, the old parish hall, which had been used since 1869, is being rebuilt on the same site, just outside the gates of the church in Church Hill. The new hall, the St John’s Parish Centre, was completed early in 2018 and dedicated for use by Bishop Harold Miller on 21st January.