Different iterations of the Skopje Kale (Kale being the Turkish word for fortress) have existed on this site since the 6th century. The fortress is located at the highest point of the city, overlooking the still waters of the Vardar River.

The first fortress is thought to have been constructed during the reign of Emperor Justinian I. It was built from materials taken from the Roman city of Skupi after the city was destroyed by a massive earthquake in 518. However, very little is known about the early life of the fortress or what life was like inside the fortress or its garrison. 

Construction work continued on the fortress throughout the 10th and 11th centuries over the Byzantine remains. In 1346, while at the fortress Stefan Dušan crowned himself emperor, and appointed Skopje as the new capital of the Serbian Empire. Sometime during Ottoman rule, the fort fell into a state of neglect and was left completely empty.

During the 19th century, warehouses, arsenals, a military hospital, and prison were discovered inside the fortress. The fortress was greatly damaged during another earthquake in 1963, which left most of the defensive towers and buildings in rubbles.  

In September 2010, the southwestern wall was restored. The completion of this work coincided with Macedonia’s Independence Day.

During an excavation of the fortress, the foundation of a 13th-century church was discovered within the fortress. A project was announced to restore the ruins as a church/museum. Albanian groups belonging to the Democratic Union for Integration claimed that the site contained artifacts relating to their Illyrian ancestry, leading to a dispute over rights to the area and violent outbreaks. The project was eventually abandoned. 

Today many unfinished, now almost ruinous, building projects can be seen scattered across the fortress complex.