The name "Wainfleet" is derived from , a stream that can be crossed by a wagon (compare with 'wainwright', a maker of wagons). The town stands on or near the former Roman settlement of "Vainona". Two tumuli, one to the north and one to the south of the town, are of unknown origin, although it has been suggested that they could be Viking or Roman. A number of coins from the period have been found in the vicinity. In Domesday Book, Wainfleet is referred to as 'Wenflet'.