In the early years of the nineteenth century there was no organ and "the music was provided by four or five men in the gallery under the tower, with bass-viol, flute, oboe and clarionet". There is evidence of a small instrument situated in the west gallery, which was moved to the south side of the chancel at the time of the 1861-2 restoration, when the gallery was removed. This instrument survived for another thirteen years and was replaced with an organ of 2 manuals, 11 stops and 3 couplers by Auguste Gern of Notting Hill, London. The cost of the instrument was £229.10s - raised by subscription, the sale of the old organ realising £30 towards the total.
In November 1908 it was decided to replace Gern's instrument with a "more modern and powerful one". Messrs. Morgan and Smith,Ltd., of Brighton supplied an estimate of £500 which was accepted by the PCC, the Gern organ being moved across the churchyard to the Baptist Church in Broad Street, where it remained until the early 1970's when the church was demolished. Members of Seaford Museum then acquired this organ and from there we think through the Dutch Organ Builder Taco Boersma eventually found a home in Holland.
The new organ was given by Mr and Mrs James S. Burroughes, and dedicated in July 1909. In 1965 the organ was rebuilt at a cost of £6,153 by Hill, Norman & Beard, the opening recital being given during the re-dedication service by Dr Francis Jackson, organist of York Minster.
During October and November 1989 the organ was cleaned and overhauled by Hill, Norman & Beard. The cost of this was £12,560. In February 2002 a new Trumpet stop was added to the Great organ to replace the one removed in 1965, the 58 pipes being made and voiced by F.Booth & Son Ltd. of Bramley Leeds. Trevor Reed of Lewes carried out the building of the organ wind chest and the installation. (Hill,Norman & Beard having by this time ceased trading). The cost of nearly £8000 was substantially met by a bequest left in 1993 by Sidney Thompson, Deputy Organist for thirty years. The remainder was raised by members of the congregation within a month of an appeal being launched in 2001. The Great organ Trumpet is situated in the Chancel arch above the organ console, making the total number of organ pipes at Seaford Parish Church approximately 1620. Read more about the specifications of the organ in St. Leonard's, see below.