The village name first made an appearance in the Domesday Book of 1086 when it was called Estone\, which in modern English means "eastern estate": possibly a reference to the village being an estate belonging to the manor of Aylesbury. However by 1237 the village had gained its own manor, which was owned by the de Clinton family, hence the name at that time of Aston de Clinton. A modern descendant of this family is Bill Clinton, former President of the United States of America who once visited the village during a business trip to nearby Chequers.
In 1853 Sir Anthony de Rothschild (1st Baronet) 1810-1876 completed the purchase and modernisation of Aston Clinton House and extensive estates in the area. A large number of worker's cottages were built, and two schools and a village hall set up under Rothschild patronage. On the death of Lady Louise de Rothschild in 1910 the house was bequeathed to the local authority for educational purposes and thus turned into a school.
During the Second World War Aston Clinton House was hit by a stray land mine dropped by enemy aircraft and was completely demolished. The local authority kept hold of the land, however, and today the estate is used as a residential training centre for young people. Many of the original ornamental features of the extended garden still remain, incorporated into the site now called Green Park.
Traditionally there were three hamletss within the extensive parish borders of Aston Clinton in addition to the main village. Two of them, Longmore and Dundridge are still part of Aston Clinton parish, though St Leonards is now considered by many to be a parish in its own right.
Property value in the village is set to rise now that the Aston Clinton Bypass has been opened. The new road means that traffic from Aylesbury to London via Watford that previously went through the middle of the village is now diverted away from it.
The Aston part of the village name was used in the company name of the car manufacturer Aston Martin, after co-founder Lionel Martin had great success in the hill climb competition up Aston Hill. A plaque now marks the site.