The pipe organ is situated in the chancel. The organ has three manuals and a pedal department with 19 stops.
It was originally built in 1884 by Brindley & Foster Ltd and installed in a private house. It was installed in the Good Shepherd in 1905 having been bought by the Rector for the church for £400.
It has undergone several major rebuilds, the latest in 1967 by Henry Willis IV. During this rebuild the console was moved from beneath the pipes to its current position on the right of the chancel.