The current main station is built on the site of the western side of the former Magdeburg Fortress.

Several competing railway companies had built lines to Magdeburg between 1839 and 1849, each with their own stations.

As the existing railway facilities in Magdeburg became more inadequate the construction of a central station became more urgent.

Both the city of Magdeburg and various railway companies conducted lengthy negotiations with the military with the objective of buying the grounds of the disused fortress.

The Magdeburg-Leipzig Railway constructed the eastern entrance building in the style of a Tuscan palace between 1872 and 1882.

As an infrastructure building, the central station was subject of heavy bombing during World War II.

At the end of March 1946, the restoration of the electrification had been completed on the rail networks in the Soviet occupation zone.

In 2003, the pedestrian tunnel was extended to connect the various platforms to an entrance on the western side of the station.