The station was an important link between the western part of the Netherlands and the north and east of the country until December 2012 when the Hanzelijn opened.

It was called Amersfoort NCS and is located next to the railway tracks 200 metres (656 ft) east of the end of the platforms of the current station.

This first station opened as part of the Utrecht–Kampen railway ("Centraalspoorweg"), which runs from Utrecht via Amersfoort to Zwolle and Kampen.

Since December 2012 and the opening of the Hanzelijn, trains from The Hague and Amsterdam now travel via Lelystad to Zwolle, avoiding Amersfoort.

A new fly-under was opened on 18 October 2013, after two years of construction, to allow trains from Hilversum to access Platform 1 without crossing the other lines.