When the level of the line to Berlin was raised in the Bergedorf area in the 1930s, a new station building was built in 1936-37, from which the trains of the Hamburg-Bergedorf Railway branched off.

As this line was closed in the 1950s and the connecting track between Bergedorf-Süd and Bergedorf station was dismantled, some of the unused railway property was developed as a park-and-ride area in the early 1990s.

After the Second World War, the importance of the line for long-distance traffic to Berlin fell sharply as a result of the division of Germany, so that in 1958 the S-Bahn was extended to Bergedorf station.

A dispatcher's signal box (code named Bfs) was built at the eastern end of the station; S-Bahn operations between Rothenburgsort and Aumühle are controlled from it.

As a result of the land released, the new central bus station was moved closer to the tracks, which accommodated an extension to the CCB shopping centre.