The station was opened in 1846 and quickly became a major transport hub.

In 1866 this was followed by the first section of the Frankfurt–Bebra railway to Bad Hersfeld and in 1875 by the line to Göttingen.

The present station building was built in 1869 on an island surrounded by rail tracks.

It experienced a small decline in importance with the opening of the Berlin curve in 1914, connecting between the Frankfurt–Bebra line and the Thuringian line and avoiding the reversal previously required in Bebra.

After World War II traffic in the area Bebra shifted more in a north-south direction as traffic heading east was disrupted by the nearby Inner German border.