Henry Willis built an organ for the church in 1895, retaining the imposing organ case by George Gilbert Scott. The instrument was much rebuilt over the years and, by the end of the twentieth century had become unreliable. In 2009, Harrison & Harrison built a new organ of four manuals and 63 stops, retaining the Scott case and incorporating some 30 surviving Willis stops.

The organ is situated in the former St John’s Chapel, south of the chancel and at the head of the south nave aisle. In this position it gives effective leadership in the nave as well as accompanying the choir in the chancel. The Great Organ speaks west into the south nave aisle, in a new case; the Choir and Solo Organs stand within the Scott case in the chancel; the Swell Organ has shutters facing in both directions. The console is placed on the north side of the chancel.