The station was established on 25 July 1889 as the terminus of a branch line from Munich opened by Lokalbahn AG.

[3] On 1 July 1912, was the line was extended with the opening of the Mittenwald Railway and Garmisch-Partenkirchen was now a through station.

A special feature for decades was the operational stop for Austrian through trains between Innsbruck and Reutte.

This was necessary so that trains could reverse direction in Garmisch-Partenkirchen, but passengers were not allowed on or off, which would have required customs and immigration clearance until the implementation of the Schengen Agreement.

The station area is bordered to the east by Bahnhofstraße and to the west by Weitfelderstraße and Olympiastraße.

The entrance building was modernised and renovated in the late 1990s and it is located on the eastern side of the railway facilities towards Partenkirchen.

Most of the trains from Munich are divided in Garmisch-Partenkirchen, with one part going to Mittenwald or Innsbruck and the other to Reutte.