A lighthouse was first established at Flamborough by Sir John Clayton in 1669, but was never kindled. The name Flamborough was first thought to be derived from it being the place of the flame, but in the domesday book the word is spelt "Flaneberg", possibly from the Saxon "Flaen" meaning a dart, which the shape of the headland resembles.
The present lighthouse, designed by architect Samuel Wyatt, was built by John Matson of Bridlington in 1806 at a cost of £8,000. It was first lit on 1st December of that year. The original lighting apparatus was designed by George Robinson and consisted of a rotating vertical shaft to which was fixed twenty one parabolic reflectors, seven on each of the three sides of the frame. Red glass covered reflectors on each side, giving for the first time in lighthouse characteristics two white flashes followed by one red flash. This was an innovation quickly adopted elsewhere. The lighthouse was oil-burning, with an equivalent candle power of 13,860.