The organ in St. Luke's Church is as historically significant as the church itself. The first instrument was loaned to the church in 1817 by Thomas Armat, in whose house St. Luke's Church was organized in 1811. By 1819, the congregation had grown, the first church building had been erected, and a second instrument had been purchased to replace the one loaned.  In mid-summer 1841, it was determined that this organ could no longer be kept in proper tune and order. The vestry was responsible for including the purchase of a new and larger instrument, along with the planned renovations to the church building.

Ten years later, the church and the organ chamber were enlarged; but after only six years, these improvements were known to be inadequate, and the idea of building a new church was proposed. In 1876, another organ was built, St. Luke's fourth, in the present Church.

The current church building, seventeen years in construction, included the initial phase of the present organ. It was used in service for the first time on Easter Sunday, March 25, 1895.

The installation of this instrument generated a notable change in the art of organ building throughout the United States. Details of both the mechanical and the tonal constructions were entirely unknown in this country up to that time. These features were immediately copied by the American organ builders. The result was that this new organ made possible the qualities evident in such instruments as the organs at the Cathedral of St. John the Divine, the City University of New York, St. Paul's Chapel at Columbia University, and many others.

​

Over the last century, the organ has undergone many enhancements and expansions. An important one was the addition of a console which enables the tower bells and carillon to be 

played therefrom. The organ was completely revitalized in 1956. Later, the tower bells were and the Trumpet en chamade was added.

​

Today, the great organ at St. Luke's Church includes between 2,500 and 3,000 pipes and remains among the rarest and most magnificent church instruments in the world. Emery Brothers are the current curators of the organ.