St John's was initially built as an independent chapelry of the parish church of Barford St Michael, and remained part of the ecclesiastical parish. However, the two lie in different hundreds separated by the river Swere. The parish of Barford St Michael is in Wootton (North) hundred, and Barford St John is technically in the parish of Adderbury in Bloxham hundred. Adderbury was the mother church over a wide area in the Middle Ages. From 1014-5 land at Adderbury had been granted to the bishops of Winchester. Between 1038 and 1044 Bishop Aelfwine leased estates to Osgod for life, but by 1086 it was back in the hands of the bishop of Winchester. In 1284 Adderbury was one of the manors confirmed to the See of Winchester. In 1086 the manor of Barford St Michael was held by Robert d'Oilly of Oxford. Barford St John's history is difficult to untangle from these two neighbouring parishes.
St John's is now in the benefice of Barford St John and Barford St Michael, together with Deddington and Hempton.