A stone keep was built on the spot in 1100 by the Eppstein family and expanded into a castle around 1117 to protect the town of Braubach and to reinforce the customs facilities. It was first mentioned in documents in 1231. The Eppsteins were a powerful family in the region, with several members becoming archbishops in Mainz and Trier. In 1283, Count Eberhard of Katzenelnbogen bought it and throughout the 14th and 15th century the high noble counts rebuilt the castle constantly. In 1429 the male line of the Counts of Katzenelnbogen became extinct, and the territories went to the Count of Hesse, who expanded the castle to accommodate artillery and added the round towers of the outer curtain wall.
The French emperor Napoleon seized then abolished the Holy Roman Empire in 1806. He gave the Marksburg to his ally the Duke of Nassau for his service. He used the castle as a prison and as a home for disabled soldiers. After the Austro-Prussian War of 1866 the Duchy of Nassau became a territory of Prussia, which took ownership of the Marksburg.
Finally, it was sold in 1900 for a symbolic price of 1,000 Goldmarks to the German Castle Association, which had been founded a year earlier as a private initiative to preserve castles in Germany. The Marksburg has been the head office of this organisation since 1931.
In March 1945, the castle was badly damaged by American artillery fired from the other side of the Rhine.