There is evidence of human occupation at the Headland extending back to the Mesolisthic, or middle Stone Age period (c 10,000 - 4,000BC). Evidence of this can be found at the wealth of archaeological sites and monuments found along the coastline from Speeton to Sewerby.

Of these archaeological sites the most enigmatic, is Danes' Dyke, a hige ditch and bank earthwork running for 4km across the whole of the Flamborough Headland, from the nature reserve in the south to Cat Nab on the Bempton Cliffs in the north. It consists of two constructed features, a flat-topped bank and a west-facing ditch. The bank was constructed from earth, stacked turfs and chalk rubble, much of which would have come from the ditch. Undoubtedly constructed as a defensive feature, it would have posed a formidable barrier, topped with a wooden palisade fence. Although no exact date has been given to its construction, comparisons with other post Roman earthworks of a similar size have been made. In particular with Aberford Dykes in the West Riding, which has been dated back to the Dark Ages. Today, Danes Dyke is a Scheduled Ancient Monument of national importance.

Flamborough Head is also littered with the remains of wartime archaeology, from pillboxes to barrage ballloon fixture points; each one reveals another story about times past.