This single manual Bates & Son organ is the only one known to remain in NSW and is housed in a delightful gothic case of gabled towers with pinnacles and featuring seventeen dummy gilded pipes. Over the years a number of modifications and changes have been made to the organ. A Heritage 2001 Programme Grant of $10,000 was received in 1999 from the N.S.W. Heritage Office towards the cost of restoring this fine instrument to a more original specification.

A Piano was dedicated in 1981 to the memory of Michael Brien, who with his wife Bertha, had devoted their lifetime to both music and the Sunday School, and was paid for by bequests, gifts and the St. John's Musical Society. The Piano has now been replaced by an electronic keyboard and the O’Brien Piano has been moved to the hall.

The music for the earliest services was provided by three flautists – Thomas Cook, Thomas Richardson and William Henry Simpson. In 1855 a Crown Pedal Organ, made by Geo. P. Bent Company of Chicago USA, was installed; this Pedal Organ is now an exhibit in the Camden Museum.

William Macarthur would complain about the quality of the music. The gallery for the organ and choir, at the west end of the nave, was built in 1861 by John Le Fevre to the design of Edmund T. Blacket, and paid for by public subscription. The organ was purchased in England about the same time and was a gift of Emily Macarthur, the wife of James Macarthur. Henry Pollock Reeves, the schoolmaster, was the first organist and continued for 33 years.