The investor and operator was the Austrian Northwestern Railway (Österreichische Nordwestbahn, ÖNWB), the project was taken over by the main architect of this company, Viennese engineer Carl Schlimp.

Jihlava railway station was erected on a slope north of the city centre from the ÖNWB's decision, this distant location was then widely criticized by residents and representatives of the town hall.

In the years 1890–1900, the railway station underwent a major reconstruction and modernization in order to serve the growing volumes of rail transport, freight especially.

During the subsequent modifications extending until 1912, a loading ramp, a waterworks, a laundry room, an ice cellar, a reception building, a barracks, a shed with a load, a ramp, a kerosene depot, a coal slide, a coal cellar, a transfer hall, a workshop, a carriage house for 20 locomotives, coal sheds, wood warehouse, stock material, station warehouse, farm sheds, wooden loading ramps, clerical and service residential buildings.

Since 1908, the electric "malodráha" (tram line) has been running from the center to the station after a wooden bridge over the Jihlava river has replaced a solid Art Nouveau concrete structure.