Originally, Wicken Bonhunt may have been two separate communities, and the name possibly derives from old English for dairy farm (wic, pl. wicum) and huntsmen liable to be summoned (bann-huntan).
Wicken Bonhunt is listed in the Domesday Book as the manors of 'Wica' and 'Banhunta', with 23 households, nine villagers, 11 smallholders and three slaves. In 1238, it is referred to in subsidy rolls as 'Wykes Bonhunte'.
Signs of this early settlement include the 10th- or 11th-century former Chapel of St Helen in the grounds of Bonhunt Farm close to an M11 motorway flyover. It is believed to be one of the oldest surviving buildings in the east of England, and an annual service is held at the site. A middle Saxon settlement of some size was excavated in the fields close to the Chapel in the 1970s, during the construction of the M11, with signs of an early settlement having been spotted in 1967 by a local archeologist. Excavations found evidence of around 30 structures, including a long room, and artefacts retrieved from the site led archeologists to believe this could have been a royal manor.Parts of the Parish Church of St Margaret, including the chancel, are early 13th century, but there was extensive restoration and rebuilding in the 1850s in 14th-century style. It is a Grade II* listed building. The interior includes a font that is thought to date from the 12th century.