Brühl station was opened on 15 February 1844 by the Bonn-Cologne Railway Company (Bonn-Cölner Eisenbahn-Gesellschaft, BCE) on the occasion of the visit of Queen Victoria and was from the beginning the most important stop between Cologne and Bonn.

The station building was built on the first single-track line in sight of the Augustusburg Palace to a design by Johann Peter Weyer.

In particular, it included the construction of a four-metre-high (13 ft) embankment to enable the removal of level crossings with other transport routes.

In a railway accident at Brühl on 6 February 2000, nine people lost their lives and 149 more were injured when a train running from the north on the opposite track at excessive speed ran on to the eastern siding and derailed.

As part of the North Rhine-Westphalia modernisation campaign of 2006, the access tunnel to the platform was widened and the stairs were provided with wheel chair lifts.