A railcar hatch control system and method for operating railcar hatches of a multi-railcar train is disclosed. A multi-railcar train may have a locomotive and a plurality of railcars having railcar hatches that can be opened and closed. The system and method may include displaying railcar identification information for the railcars on an operator display device, and receiving selections of railcars from an operator that will have a railcar hatch operation performed thereon, such as opening or closing the hatches. The railcar hatch operation is input, and the system and method control the railcar hatch operation being performed only on the selected railcars, and not on the railcars that have not been selected by the operator. The system and method may have operator interfaces devices at an operator station of the train, or at a remote location or on a remote device that communicates wirelessly with the train.