St Clether parish has had three churches - the present Holy Well Chapel and, later, two on the present church site.   St Clether (or Clederus) built his hermitage beside a spring in the Inny Valley and erected a 4th century granite altar.   The chapel is the largest holy-well chapel in Cornwall, serving the community as its church until the 12th century, when a church was built on the site of the present building.

Very little is known about St Clether, save the tradition that he was one of the 24 children of a Welsh chieftain named Brychan, all of whom became church founders in Cornwall, Wales or Devon.

By the 19th century the hermitage (chapel) building had become a ruin, but it was rescued by the Rev Sabine Baring-Gould, a famous Victorian archaeologist and the writer of the hymn "Onward Christian Soldiers".   He organised its rebuilding in 1895.   Water from St Clether's Holy Well, which originates in a spring with a stone canopy north of the chapel, passes through the chapel itself and then out through the south wall.   Services are occasionally held there and the chapel is a popular destination for walkers, particularly in the summer months, lying half-a-mile west of the church, and accessed by a footpath between steep, grassy banks.

The current church has a 15th century tower, but apart from the tower the building was largely replaced in 1865.   A special feature is the simple Norman font, which has a round bowl and rim, and a shaft with "rope" banding.