The church was founded before 1100 with the village of Wilton being mentioned in the Doomsday Book as Wiltune. It is believed that the monks from Lindisfarne paused here on their journey with the body of St. Cuthbert, which they were trying to keep safe from the marauding Vikings. (St. Cuthbert's Wilton is included in the list and map of these journeys displayed in the cloisters at Durham Cathedral where the tomb of St. Cuthbert can be found.)
When the church here was founded it was in the care of the Monks of Guisborough. In-between 1340-49 the Norman Chancel was taken down and an Early English Chancel erected and consecrated in 1349, after this alteration; it is a belief; that the name of the church was changed to St. Cuthbert.
During the Dissolution of the Monasteries the Monks at the Priory of Guisborough was disbanded and land and endowments were confiscated by the Crown, by 1614 the church was in a bad state of repair. Then in 1850 a part restoration of St. Cuthbert's Wilton took place with help from Sir J H Lowther and his wife of Wilton Castle. The original stones were used wherever possible - some pre-Norman.
Then in 1907/8 another renovation, with the original stones being taken down, numbered and re-used in the reconstruction.
There are indentations on the original stones, within the church, legend has it that they were made when Cromwellian soldiers sharpened their weapons. However it was the custom for archers to sharpen their arrow-heads on the wall of their church in the belief that this made them more effective against their enemies. Wilton also suffered, over the years, from Scottish raiders.
The old box pews (to a height of over five feet) were replaced with plain oak pews and a new font was placed in the West end. Three Norman windows (1340-50 Early English) in the North wall were restored into use.