The village name is Anglo Saxon in origin, and means 'Padda's fortress'. In the Domesday Book of 1086 the village was recorded as Pateberie.
The village had the distinction in Domesday as being one of the few villages in the country still owned by a native rather than a Norman family. It remained in this family (who later took the name 'de Wolverton' after the village of Wolverton, Milton Keynes) until 1442 when it was sold to All Souls College, Oxford.
During the English Civil War Padbury was the site of a skirmish between the Royalist and Parliamentarian forces. The Royalists won on this occasion, and the burial of eight Parliamentarian soldiers is recorded in the village's burial register for July 2 1643.