The Organ was built in 1883 by J W Walker & Sons of London, one of the finest of all Victorian organ builders. It was originally buillt for St Saviour's Church, Eastbourne, but was then installed at St John's and dedicated on St. James's Day, 25th July, 1883. It is of considerable historic interest.

There are three manuals, the Great having twelve stops, the Swell twelve and the Choir eight. the Pedal Organ has eight stops although the pipes for some are extended from the Great Organ. There are about two thousand three hundred pipes in all. A major rebuild was completed in March 2012. The instrument is able to do justice to a wide variety of music, from sacred to secular.