The station was opened on 10 January 1861 at the same time as the branch line from Siegen to Betzdorf, which is now part of the Sieg Railway.

The south-western part of the site, the railway depot in the preserved buildings and the tracks that are numbered from 50 were the terminus of the Cologne-Mindener Eisenbahn-Gesellschaft (CME), which was responsible for the construction of the line, but was taken over by the Prussian state in 1880.

After being nationalised in 1882, its facilities for the maintenance of rolling stock became a repair shop, which were later demolished and replaced by highway B54, locally called Hüttentalstraße.

In this context, no separate track was provided to the former main post office, since letter centre 57 had been relocated to the autobahn.

The founding of the Eisern-Siegener Eisenbahn (now part of the "Siegen-Wittgenstein district railway") and the connection of its central Eintracht station to the Siegen freight yard was a state initiative, which participated from the outset, as a result of which track 52 was used as a transfer track without an overhead line until it was renovated around 2020.

It was not until 1 December 1915 that the Dill Railway was extended, giving a direct rail connection to Haiger (and thus Frankfurt), because its construction had previously been considered too difficult, not militarily urgent and could not be financed.

As a railway junction in a centre of iron production, steel production, tool manufacturing and mechanical engineering, the Siegen junction and railway infrastructure was an important strategic target of the Allied bombing raids, especially on 16 December 1944 and until March 1945, during which 90 percent of the city, many tracks, but not the entrance buildings, were destroyed.

With the division of Germany in 1945, only the traffic flows in the north-south direction continued to develop, which led to the Hagen–Giessen axis, including Siegen station, being electrified in 1965, but the Sieg Railway did not follow until 1980 and the Betzdorf–Haiger railway was no longer considered important and in fact one track was dismantled.

Between the sidings on Heeserstraße and the main post office, a central "Sp Dr S600" signal box was built in the 1980s for the triangular junction and sections of track up to and including Geisweid, Brachbach and Rudersdorf stations.