The station was opened by the York and North Midland Railway in October 1847. It was on the last section of the Hull to Scarborough line to be opened; Hull to Bridlington had been achieved in October 1846, and southwards from to was in use by the same month. The station was located immediately north of the gated level crossing that spanned the road from Marton, and had a G T Andrews designed building. The extra effort put into Flamborough station was due to the influence of the Yarburgh family of nearby Sewerby Hall, who used the station. It was located north of Hull and south of Seamer. The station had a small goods yard which was the nearest loading point for fish landed at Flamborough. Previous to the opening of the railway, carts of fresh fish used to travel the south to Hull. Even so, the demand of transporting the fish the to the station from Flamborough Head, was seen as a bar to good business. The distance between the station and coast was also seen as detrimental to the burgeoning tourist trade and in the 1890s, a branch was proposed by the residents, something which the North Eastern Railway considered, but refused to undertake. The goods yard handled mostly fish, corn and coal. The NER had a policy of making their stationmasters the agent for the handling of coal, which guaranteed traffic for the railway company. The station master at Flamborough in 1920 had an annual wage of £230, but the profit on the coal handled at the station was £95. Wagons loaded with fish were allowed to be attached to Hull-bound trains via gravity whilst the Hull service was waiting in the southbound platform. Cattle and stone were also handled at the station; the chalk cutting just to the north of the station was opened out into a quarry in 1876. During the First World War, the line was singled as an economy measure. Double track was restored in 1923, though three years after the station closed, British Rail singled the section between and Filey. The station was host to a LNERcamping coach from 1935 to 1939. The station closed to goods traffic in August 1964, and closed completely on 5 January 1970. In 1976, the station was given Grade II listed building status.
