The village is mentioned in the Domesday Book as Hotone and under the ownership of Richard de Vernon. Sir William Stanley obtained a licence to crenellate in 1487 but built a half timbered manor house 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 Hooton Park airfield was built to train pilots 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. The Hooton Park Trust was formed in 2000 with the aim of restoring the remaining Grade II* listedhangars, but with little success to date.
Until 1933, Hooton was part of the parish of Eastham in the Wirral Hundred. The population was 91 in 1801, 110 in 1851 and 200 in 1901.