Part of the improvement to the church carried out during the summer of 1885 was the provision of a church organ.
The organ was built and installed by August Gern of London. He was a German but trained in the famous French organ-builders of Cavaille-Coll and absorbed the French style of organ-building, providing a romantic tone to Gern organs. He came to Britain to build one organ and stayed on to build many more, only about ten of which were built in Scotland.
The organ, which was constructed on a new tubular pneumatic system blown by a new patent hydraulic engine, is contained in a handsome case which was situated behind the original pulpit, while the console is located within the body of the church.
In 1885, the church was being equipped with a new oak pulpit which had to be brought forward to allow the organ to be located behind it and between the Burne-Jones memorial windows.
The organ was inaugurated on Friday 2 October 1885 with a recital by Mr Joseph Bradley, organist with the Halle orchestra in Manchester. The large audience included representatives from the Presbytery, the Provost, Magistrates and Councillors, and prominent businessmen of the town and their ladies.
The organ during its lifetime has had an unfortunate history of defects and repairs. In 1889, the organ engine had to be replaced and in 1896 Mr Grant, a church elder, had to raise with Mr Gern the question of organ repairs when he visited London. The repairs were duly completed in 1897 which necessitated a new engine being fitted at a cost of £200. However, in December 1898, the organ was seriously damaged by damp penetration of the east gable during a severe storm which required expensive repair work on the organ in 1899.
In 1903, the Session had to meet Mr Gern regarding the dangerous condition of the centre tier of organ pipes and, in 1904, during improvements to the church including the installation of electric light, the dangerous organ pipes were replaced. In 1907, Mr Gern, while re-tuning the organ, reported a defect in the blowing action which was repaired, and in 1911 new organ machinery had to be installed.
In 1963, just when church renovations were under consideration, a burst water tank flooded the organ chamber and it cost £3,000 to have the organ rebuilt by Jardine & Co, Manchester. During the renovations of the church in 1968, the organ console was moved to the side of the church, its present location. Finally, during the fire in 1986, several of the organ pipes were melted due to the intense heat and the organ was damaged to such an extent that it cost around £17,000 to repair by Messrs Rushford & Dreaper, organ builders, who for insurance purposes valued the church organ at £175,000. It is considered by organists to be one of the best instruments in the district.
Building work in the church in 2005, when the interior was reordered to face west, was carried out without due care by the workmen, and resulted in the organ needing further repair. This was completed just before the building was closed as a place of worship by the Church of Scotland on 7th November 2010. The "B" listed church was put up for sale in August 2011 and a Trust, formed for that purpose was successful in acquiring it to maintain it for community use as a concert hall, community resource, heritage centre and for continuing worship.
When Kirkcaldy Old Kirk Trust negotiated the purchase of the closed building in August 2011 the Gern organ had been in a state of disuse for a few months in a winter where the temperature was in minus figures. However once the building was re-occupied, the organ with a few minor adjustments was fully working. It is used regularly by visiting
organists. A few complaints about the console lighting were easily rectified by fitting LED lights.
In 2018 a young man was offered the position of Organ Scholar by Kirkcaldy Old Kirk in partnership with St. Peter's Episcopal Church around the corner.
In 2019 as part of the Old Kirk's 775th Anniversary celebrations, an organ recital programme was introduced for the year Easter 2019 - Easter 2020. On organists' advice, the console was not moved into view for these but an organ camera was installed to show the organist on the main screen at the front.
The building is much used by theatrical groups, orchestras, choirs and other community organisations which are keeping the building alive and these organ developments are maintaining the organ in situ.