The earliest known record of Shipton-on-Cherwell is from AD 1005, when an estate at Shipton was granted to the Benedictine Eynsham Abbey. Shortly before or after the Norman conquest of England an estate of five hides at Shipton seems to have been transferred from Eynsham to another Benedictine religious house, Evesham Abbey. However, after the death of Evesham's Abbot Æthelwig in 1077 or 1078 William of Normandy's half-brother Odo, Bishop of Bayeux took Shipton from Æthelwig's successor Walter. By the time of the Domesday Book in 1086, Odo had only 2½ hides at Shipton and these were let to Ilbert de Lacy. Hugh de Grandmesnil held the other 2½ hides and it is not clear whether the estate had been divided before or after the Conquest.
Shipton Manor House was built in the 16th or 17th century. William Turner lived there from 1804 with his uncle, also William Turner. He was married there in 1824 and is buried in the churchyard with his wife. In 1896 a memorial chancel screen was installed in the church, with a brass plaque reading "Erected in memory of William Turner of Oxford, Water Colour Painter and architect of this church."
In the 20th century Richard Branson owned the manor house and turned it into The Manor Studio, a recording studio for Virgin Records. Albums recorded there included Tubular Bells by Mike Oldfield in 1972–73 and Born Again by Black Sabbath in 1983. In 1995 it was closed as a recording studio by EMI, by then the owner of Virgin Records. It is now the country home of the Marquess of Headfort.