The church of St Mary Magdalene was built in 1837/8 and was the first church designed by the renowned architect Sir George Gilbert Scott, a nephew of the then incumbent Rev Samuel King. The church was built to replace a medieval church about two miles away in what was a former site for Flaunden village; nothing now remains of this earlier church or settlement. The church was consecrated on 19th June 1838 by the Bishop of Lincoln.
The church is built of brick and flint, with a single nave, a small vestry, a gallery at the west end and a turret containing a clock and one bell. The bell is dated 1578 and came from the old church, as did the font and medieval tiles which were used to pave the entrance porch. These tiles were once covered with patterns and designs such as lions, kings, queens and saints, but they are now very worn.
The church is also recognised as an early example of the revival of constructional polychromy in a church building, using brick and other materials to mark features in the exterior walls.
The interior of the church was substantially altered in the winter of 1946/7, with the font being repositioned, the number of seats reduced, screens installed to form a separate entrance and baptistry and electric lighting installed.
The stained glass window in the East window, depicting the resurrection of Christ, dates from 1958 and was the work of artist John Hayward.
Flaunden was originally a “perpetual curacy” under the church of Hemel Hempstead, with curates sent from there to perform the duties. It later became a Vicarage and then a Rectory, when Flaunden was united with neighbouring Latimer into one benefice in 1876. Flaunden was then moved from the diocese of Rochester to the diocese of Oxford. In 1987, Flaunden and Latimer were joined with the parishes of Chenies and Little Chalfont into one united benefice.
The churchyard contains memorials to the family of Lord Ernest Hamilton (1858-1939), youngest son of the 1st Duke of Abercorn and grandson of the 6th Duke of Bedford.