A few Roman artefacts have been found locally and it is possible that the Blyth river was forded here (at Mells) as it lies on the route of an ancient trackway from Dunwich to Beccles.

Holton Hall, demolished in 1957 and replaced by a caravan park, had many famous connections to the anti-slavery movement and Barclays Bank.

In 1814 John Brewster Wilkinson the son of john Wilkinson paid for the school to be built with an endowment of £200 a year (from whites directory of Suffolk 1842) Holton also boasts a post mill, parts of which date back to the 18th century.

The mill had been left in a state of disrepair in the 1960s but was rescued and has been restored on numerous occasions since, and its sails started working again in 1996.

An outbreak of avian influenza of the H5N1 strain was confirmed on 3 February 2007, at a farm near Holton owned by Bernard Matthews.