Beit Shemesh Station was built under Ottoman rule with the construction of the Jaffa-Jerusalem railway, the first rail line in Palestine.

The location of the station remained unchanged throughout this period, at a point that now lies on the northern border of the city of Beit Shemesh, near Highway 38.

In 2006, the track was split into two for a trial period: Tel Aviv-Beit Shemesh and Beit Shemesh-Jerusalem.

Following the split it was attempted to operate double-decker passenger cars until Beit Shemesh, and IC3 systems until Jerusalem.

This has rendered the rail section between Beit Shemesh and Jerusalem inoperative until either a replacement train is found, or the line undergoes a massive renovation.