Gunzenhausen station was opened on 20 August 1849 in conjunction with the Oettingen–Gunzenhausen section of the Ludwig South-North Railway.

On 1 July 1859 the line to Ansbach was opened to connect the city to the Ludwig South-North Railway.

On 1 October 1906, a new section of the Nuremberg–Augsburg railway was opened, which ran directly to Treuchtlingen, making the detour via Nördlingen and the Franconian Jura unnecessary.

Deutsche Bundesbahn closed passenger services on the Nördlingen–Gunzenhausen line on 29 September 1985 and freight operations on 1 August 1995.

Platform lengths and heights are as follows:[5] Gunzenhausen station is served hourly by the Würzburg–Treuchtlingen Regionalbahn service, operated with class 440 EMUs as the Mainfrankenbahn.

Regionalbahn services run hourly on the Gunzenhausen–Pleinfeld line between Gunzenhausen and Pleinfeld, operated with a Siemens Desiro Classic or a Alstom Coradia LINT diesel railcar.