Discoveries of Mesolithic flint implements, over 5,000 years old, a bronze axe head, a Celtic pot and various Roman coins shown that people have lived in and around Kingston for many thousands of years. Nevertheless it seems that there was no permanent settlement until Anglo-Saxon times, when a royal vill was established. The name of the village, in its earliest form Cyningestun, derives from this and means "King's farm" (Charlton in the adjacent village of Bishopsbourne comes from "Ceorl's - servant's - farm"). To date no buildings have ever been identified from this period, but over 300 Saxon graves from the pagan period lined the old Roman road, now the A2 main road between Canterbury and Dover.

The fanciful local tradition that one of the earthworks on the Downs was one of Julius Caesar's camps can be disregarded, likewise the notion that one of his battles against the Britons was fought near the Nailbourne, the intermittent stream that runs below the village.

There are occasional references to Kingston in Anglo-Saxon documents. In one of the most notable, Palmstead, once counted as part of Kingston, is mentioned in a grant of land by King Offa, A.D. 791, to Christ Church, Canterbury, for the pannage of their hogs.

King John camped on the Downs in 1213 with an army to meet a threatened invasion by Philip, king of France and in the reign of Henry III, Simon de Montfort, Earl of Leicester, assembled another army to oppose the landing of the king's wife, Queen Eleanor, from France.

During the Civil War, there was a skirmish between Cavaliers who occupied the church and some Roundheads, who eventually drove them off. A great service to King Charles II was done by a son of Sir Thomas Wilsford of Ileden, a country house above Kingston. Although in holy orders, he commanded a troop at the Battle of Worcester and enabled the king to escape afterwards, as a reward for which he was later given the vicarage of Lydd, Kent.