Stoke D'Abernon appears in Domesday Book of 1086 as the manor of Stoche (derived from the common Anglo-Saxon word stoc, implying a holy place).

Following the Norman conquest of England in 1066, William the Conqueror granted the manor to his kinsman, Richard fitz Gilbert, who also received the lordship of Clare.

The suffix D'Abernon comes from the surname of another Norman nobleman, Sir Roger D'Aubernoun, who was also granted land in Surrey in return for his services to William. At some point after 1086, the de Clare family granted the manor of Stoche to the D'Aubernoun family, who held it until the mid-14th century.

Two descendants of Sir Roger, Sir John D'Aubernoun the Elder (died 1277) and his son Sir John the Younger (died 1327) are buried in the village; monumental brasses of them are contained in St Mary's Church, with the one of Sir John the Elder believed to be the oldest in England.

The church, St Mary's, is Saxon with Norman and Victorian additions, and is famous for its monumental brasses, among them the oldest in the country.

Until the mid-19th century, Stoke D’Abernon lay in the hundred of Elmbridge, which gave its name to the modern-day borough.

It has its own railway station, named Cobham & Stoke d'Abernon to attract the much greater trade and use of the larger village of Cobham.

Since 2006 the village has been home to the training ground of Premier League football club Chelsea.