The organ at St John's dates from 1915 and was built by the Pyrmont firm Griffin and Leggo, who were in partnership between 1915 and 1918. They built a number of organs locally besides undertaking two major rebuilding jobs in Fiji. The pipes were made and voiced by Alfred Palmer and Sons of London.

When the church was opened in 1882, its first organ was an American reed organ... to be replaced some years laer by a larger instrument, which had been lent rent-free by the city firm of Palings.  There is a record that a small boy of six offered his services as blower without charge.  In due course the church acquired a Dresser pipe organ from St. Andrew's Summer Hill, which was later enlarged by the addition of a second manual.  It served the church until 1913 when a new one was ordered and the Dresser was sold to St. Augustine's in Neutral Bay.

An electronic pump was added in 1923 and a new stop in 1930.  In the church's jubilee year of 1932, the whole instrument was dismantled and rebuilt in its present position because "it would better balance the appearance of the church and assist the choir".  During the the work it was found that accumulated dust from the just-closed coalmine nearby had choked every part of the instrument and also that the floor beneath the organ was riddled with borers threatening stability.

Music is an integral part of public workship at St. John's and continues under the guidance of the director of music, Andrew Pell.