Scoonie Kirk has a long and fascinating history extending over 16 centuries. It is believed that the beginnings of the Kirk go back to the cave or shelter of St Ethernanus or Ethernan (Aithernie may be a corruption of his name) in the fourth century and some current excavations on the May Island relate to his Christian mission from Ireland to Scotland. The earliest known relic of the Kirk is the Scoonie Stone.

The stone which is considered to be of Pictish origin was found in Scoonie Cemetery and removed initially for safe keeping to the Kirk but handed over in 1866 to the Scottish Museum of Antiquities in Edinburgh and is now in the hands of the Royal Scottish Museums in Edinburgh.

The front of the upright sandstone slab shows a much weathered symbol of a cross which can still be seen albeit faintly and the reverse side shows a hunting scene with the elephant symbol above it.

Scoonie Kirk originally stood at the top of Scoonie Brae on the knoll which forms Scoonie Cemetery and the Durie vault in the old part of the cemetery is all that remains of the original Kirk. The area was known as "Little God's Acre".

The earliest extant record of Scoonie Kirk is dated July 1687. Earlier records were held in the Manse and in 1641 when the then Minister the Rev. Robert Cranston was conducting a service fire swept through the manse and destroyed all Session records. Other records, however, give us a fascinating insight into the life of the Kirk in Leven and so provide an interesting social history of the local community. In the 12th century the Culdees (a fraternity of Monks) of the pre Roman Catholic Church in Scotland were in possession of the Kirk and in the year 1200 Duncan, Earl of Fife, transferred through Robert, Bishop of St Andrews, the "Church of Scouni and the lands belonging thereto with tythes and oblations and with all the rights and benefits of all kinds" to the Priory of St. Andrews. On 30th May, 1243 Bishop de Bernham dedicated the Church to St Modwena. In the mid 16th Century the Church would have been taken over by the Reformed Church, the Church of Scotland, and around this time the name would be changed to Scoonie Kirk.

By the middle of the 18th. Century the building had fallen into disrepair and in 1760 it was reported to be neither wind nor water tight. The congregation used a temporary barn until the new Kirk with sittings for 700 opened in July 1775 on the present site in Durie Street. In 1822 the Kirk was enlarged to seat 1,000 and in 1883-84 a porch was added and an organ chamber built so that the present pipe organ could be installed by the French organ builder, August Gem, in August 1884.

Scoonie Kirk was at that time and continued to be well into the 20th Century one of the best remunerated charges with the Ministerial stipend coming not from congregational giving but from the "Glebe". In 1885 the Ordnance Gazetteer of Scotland reported that the living in Scoonie was worth 1;426 per annum - a not inconsiderable income in those days.
In 1901 it was decided to extend the Kirk again to provide 1,200 seats for the growing congregation in the "Old Parish". The South wall and organ chamber were retained in the design produced by the celebrated architect, McGregor Chalmers, whose trade mark can be clearly seen at the base of the North East pillar inside the Kirk. A new steeple was strapped on to the old steeple and the kirk extended to incorporate both a long gallery in the North and a small gallery in the West. The clock with faces to the South and West was also incorporated in the new steeple. The rededication of the enlarged Scoonie Kirk was held on Saturday 6th August 1904 and the cost of the rebuilding is recorded as £5,200, a considerable sum of money at the time.

The steeple was reconstructed in 1985 and much of the eroded sandstone was replaced after funds were raised by the congregation.