It is served by about 100 trains daily operated by Deutsche Bahn and Bayerische Regiobahn (BRB).

Both lines are single track and not electrified and are served only by regional services operated by Bayerische Regiobahn.

The line would primarily carry “pitch coal” (Pechkohle, a form of lignite) mined in Peißenberg.

On 29 July 1876, the Bavarian state parliament approved the route, allowing construction to start in 1878.

In the early 1870s planning began for a railway line from Augsburg to the Ammersee (Lake Ammer) and continuing towards the Alps.

In 1886, the Bavarian government approved the Ammersee Railway, running from Mering near Augsburg via Diessen to Weilheim.

[5] On 1 January 1917, the Weilheim–Peissenberg line (also known as the Pfaffenwinkelbahn—Pfaffenwinkel Railway—after the Pfaffenwinkel region, which lies mainly to the west and south of Weilheim) was extended to Schongau, where it connected to the existing Fuchs Valley Railway to Landsberg am Lech.

[6] On 1 May 1925, the Pfaffenwinkel Railway between Weilheim and Peissenberg was also electrified; the electrification on this line mainly served coal transportation.

[5] During the Second World War, the Allies dropped about 250 bombs on the station during an air raid on Weilheim on 19 April 1945.

To the north and south of the main building there were single-storey extensions with flat roofs, which were the same size as each other.

In the 1900s, a further single-storey building with a hip roof was built on to the southern extension; this included a station restaurant.

During World War II, the northern part of the building was destroyed in an air raid on 19 April 1945.

West of the platform tracks were freight and storage sidings as well as the roundhouse and the turntable of the locomotive depot.

Signal box 3 was a mechanical interlocking of the Krauss class of 1925, which controlled the marshalling yard and was located at the southern end of the sidings to the west of the station.

[5] Weilheim station is served by Regionalbahn services of Deutsche Bahn trains and Bayerische Regiobahn (BRB).

The Ammersee and the Weilheim–Schongau lines are served every hour by BRB trains operated with LINT 41 diesel multiple units from Augsburg to Schongau.

In the winter, the Garmischer Skiexpress (classified as a Regional Express) also runs on weekends from Munich to Garmisch-Partenkirchen Hausberg and is formed from double-decker carriages.

In 2013, class 442 (Bombardier Talent 2) railcars replaced the locomotive-hauled carriage trains on the Regionalbahn service from Munich to Garmisch-Partenkirchen.

Intercity Express trains that run on Saturdays on the Munich–Garmisch-Partenkirchen line, ran through Weilheim station without stopping until the low platform heights of 34 cm were raised in 2016/2017.