Holzkirchen station was opened on 31 October 1857 together with the section Großhesselohe-Rosenheim the Bavarian Maximilian Railway.

On 23 November 1861 a route to Miesbach was opened so that Holzkirchen became a railway junction.

Since most of the trains went via Grafing, the Bavarian Maximilian Railway and the Holzkirchen station lost their traffic.

On 1 June 1874 another outgoing line from Holzkirchen route to Bad Tölz was opened.

On 24 November 2009, there was a motor fire in an Integral train of the Bayerische Oberlandbahn.