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.

By the year 2000 the organ was beginning to show its age and fundraising by the church social committee was undertaken to raise funds to restore or replace the organ. In 2016 an Organ Committee was formed and after a consultation with the congregation it was decided to restore the organ rather than replace it.

Michael Macdonald Organ builders were entrusted with the restoration and it was scheduled in 4 stages for summer 2019 and summer 2020. Sufficient funds were provided from the congregation, their families and friends to enable Stages 1, 2 and 4 to be completed. Stage 3 which involved the addition of further stops for the organ, which were prepared for but not added at the 1967 rebuild, was also funded from reserves. Stages 1 and 2 were completed in August/September 2019 and Stages 4 (replacement of the electrics) and 3 will be completed in summer 2020. The timetable for this will allows for the least possible disruption to services at major festivals. After the restoration the organ will be fit for many more years of service in the church.