The initial fortress was constructed during the time when the region was part of the Roman Empire. The rock formations in the area served as a natural protection, as fortified walls were practically only built from the northwest and southeast, with the yard being surrounded by rocks up to 70 m (230 ft) high from the other sides.

The Belogradchik Fortress was built by  the Romans and extended by the Bulgarian Tsar of Vidin, Ivan Stratsimir in the 14th century, building fortified garrisons in front of the existing rock massifs. During Stratsimir's rule, the Belogradchik Fortress became one of the most important strongholds in the region, second only to the tsar's capital fortress of Vidin, Baba Vida.

During the Ottoman conquest of Bulgaria, the fortress was captured by the Ottomans in 1396. They were forced to further expand the stronghold due to the intensified hajduk and insurrectionist activity in the region.

Considerable changes to the fortress were made in the early 19th century. These changes were typical for the Ottoman castle architecture of the period, a full reorganization being carried out, as well as additional expansion. Typically European elements were added to the Belogradchik Fortress owing to the French and Italian engineers that participated in the expansion.

The stronghold had an important role in the Ottoman suppression of the Bulgarian Belogradchik Uprising of 1850. It was last used in warfare during the Serbo-Bulgarian War in 1885.