On 1 April 1854 the Flensburg–Tönning line was opened by the British entrepreneur, Sir Samuel Morton Peto to a station outside the city at Holzkrug.

In 1883 the original, simple station building was replaced by a more complex design of Johannes Otzen, a famous church architect.

The Flensburg station is a particularly impressive collection of brick expressionism of the 1920s and some of its outbuildings are partially protected as monuments.

In normal usage platforms are used as follows: In long-distance transport, a Eurocity service runs from Aarhus to Hamburg via Flensburg.

DB Regio Nord operates Regional-Express and Regionalbahn services between Neumünster and Hamburg every hour.