The station opened on 30 October 1848 as Allerton , under the management of the East and West Yorkshire Junction Railway.

Goods facilities were installed on the north side of the main line, featuring a crossing just west of the entrance to the cattle dock.

The station included two sidings serving six coal cells, and flag signals controlled movements within the goods yard.

Hopperton station survived the nationalisation of the railways but saw a significant reduction in services by the summer of 1958.

The station was one of four on the line to close to passengers on 15 September 1958, the others being Hessay, Marston Moor, and Goldsborough.