The form of the churchyard suggests the existence of an Anglo-Saxon church on this site, but none of the fabric can be dated to the pre-Conquest period. In 1086 Farnborough manor was owned by the Bishop of Winchester and tenanted by Odin of Windsor. It included a church. The church was documented again in 1230, when Stephen de Farnborough was accepted as patron. The medieval dedication is not known.
The chancel was rebuilt in 1886 to designs by A. Rowland Barker. In 1900-01 Sir Arthur Blomfield & Sons added transepts, a S aisle and dormers to the nave. The S doorway was reset in the new aisle, but the opening was blocked (Keyser 1907, Pl14a; Historic England red boxes). Transepts were built to either side of the chancel in 1963-64.