The village of Arncott is made up of two areas, separated by the Bicester Military Railway. The larger neighbourhood of Upper Arncott to the south and the smaller Lower Arncott to the north.
The Domesday Book records that in 1086 William, son of Mann, held Lower Arncott. In the 12th century Roger of Caux granted it to the Augustinian Missenden Abbey to say Mass for his late parents and in 1232 the abbey sold it to the Augustinian Bicester Priory. As a result it became known as Arncot Prioris. After the dissolution of the monasteries the Crown granted Lower Arncott to Thomas Martin, of Ambrosden.
Meanwhile, in 983AD Ethelred the Unready granted the manor of Upper Arncott to the Benedictine Abingdon Abbey and it became known as Arncot Abbatis. The Abingdon Chronicle, a version of the Anglo-Saxon Chronicle, records that Adelelm of Jumièges (Abbott of Abingdon 1071–83) let Upper Arncott to the Norman barons Robert D’Oyly and Roger d’Ivry. They, in turn, granted it to Saint George’s Church in Oxford Castle. In about 1149 Henry D’Oyly transferred it to Osney Abbey, which remained lord of the manor until the church of the former Priory of St Frideswide replaced Osney as Christ Church Cathedral, then it reverted to the Crown, which sold it to the Martin family.
A Methodist congregation developed in Arncott from 1823. A Wesleyan Methodist chapel was built in Upper Arncott in 1834 and enlarged in 1847. It became Upper Arncott Methodist Church and was a member of the Buckingham, Bicester and Brackley Methodist Circuit. In 2010 it was closed and converted into offices.
A parish school was opened in the nearby village of Ambrosden in 1818 and Arncott had its own school by 1833. Both seem to have ceased operating by 1854, but temporary schools existed in both villages in 1868. A permanent parish school built in Ambrosden was opened in 1876 and in the same year an infant school was opened in the parish mission room in Arncott. In 1920 Arncott School was closed and the children transferred to Ambrosden.