In 1070 William the Conqueror granted the lands of Hooton to Adam de Aldithly. The village is mentioned in the Domesday Book as Hotone in the hundred of Wilaveston (later called the Wirral Hundred) and under the ownership of Richard de Vernon. Eventually the lands passed to the Stanley family through a series of marriages. After the Battle of Bosworth, Hooton had a new hall and the first Lord Derby in Lancashire.
Sir William Stanley obtained a licence to crenellate in 1487 but built a half timbered manor house in 1488 which survived until 1788 when it was demolished. The old house was replaced by a mansion called "Hooton Hall", built from local stone from the quarries at Storeton. Hooton Hall was designed by the architect James Wyatt in the Italian Palladian style for the fifth Baronet, Sir William Stanley. The family sold the estate in the nineteenth century after Sir Massey Stanley had gone bankrupt due to his high living. It was used during the First World War as a military hospital, but was demolished in 1935.
In 1917 RAF Hooton Park airfield was built with 3 double Belfast Hangars to train pilots for World War I from Canada and the United States. The Second World War saw the airfield utilised as a military base, and three RAF auxiliary squadrons were based there until disbandment in 1957. Much of the airfield (including the site of the Hall) was transformed in 1962 into a factory for Vauxhall Motors which as of 2015 is home to the Vauxhall Astra range of cars. In 1990 the former RAF base was leased by Vauxhall to a charity called The Griffin Trust which managed the site until 2000 when The Hooton Park Trust was formed and tasked with restoring the Grade II* listed hangars.
Hooton railway station lies on the Wirral Line of the Merseyrail network with frequent electric trains to Liverpool, Chester and Ellesmere Port, and is the junction of the lines to Chester and Ellesmere Port. The trackbed of the former GWR/LM&SR Joint branch line from Hooton to West Kirby now forms the Wirral Country Park.
- John Owen (1827 in Marchington – 1901 in Twickenham) an English vicar and strong amateur chess master. He was vicar of Hooton, from 1862 to his retirement in 1900. He played chess in British tournaments into the 1890s and performed strongly in several matches against top British players, who were essentially chess professionals.
- John Kebty-Fletcher (1869–1918) a British Conservative politician. MP for Altrincham 1910–1913, when he resigned causing a by-election. In 1912 his address was given as "The Paddock", Hooton, Cheshire.
- Sir Herbert Williams, 1st Baronet (1884 in Hooton – 1954) a British politician and Conservative MP for Croydon South 1932–1945; grandfather of Fiona Mactaggart Labour MP for Slough 1997–2017.
- Sir Doug Ellis OBE (1924 in Hooton) an entrepreneur who pioneered package holidays to Spain and former chairman of Aston Villa F.C.
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