Shipton had a parish church by the latter part of the 12th century, which seems to have been enlarged in the 13th century and received new windows in the 14th century. It was demolished in 1831 and replaced by a new Georgian Gothic Revival Church of England parish church designed by the artist William Turner who lived at the manor house.Some original materials from the original church were re-used. Crossley and Elrington state that this includes the north porch, which Sherwood and Pevsner had earlier dismissed as “free and flimsy Georgian Gothick”. Holy Cross was restored in 1869 under the direction of the Gothic Revival architect Charles Buckeridge.

The belltower has only two bells.They were cast in the middle of the 16th century and presumably came from the original church.

The original dedication of the 12th-century church was to the Holy Cross. By 1786 the dedication had been changed to Saint Mary, and by 1851 it had been changed to Saint Jerome. By 1892 the church was finally restored to its original dedication of Holy Cross. The parish is now part of the Benefice of Blenheim, which also includes Begbroke, Bladon, Woodstock and Yarnton.