Under the influence of major cultures from the Mediterranean, the process of gradual civilization of this region started in the 5th century BC. This would mark the end of Prehistory and the beginning of the Early Classical Age. Archaeological findings (pottery, jewelry, and weapons), which were discovered in several places in the region of Skopje, indicate to the direct trade and cultural contacts of different people in this region (Darden, maybe Pyon, and Ugrian) with the cultures from the Peninsula (Ancient Greece and Macedonia). Since the time of Phillip II, this region represented an important strategic point of the Ancient Macedonian State. After the expansion of the empire, a number of vital battles between Ancient Macedonia and Roman Empire were fought.

Since the 2nd century BC the Skopje region, as well as all of Macedonia, fell under Roman government control. The city received the name Scupi - after the name of an older local settlement. Ever since then, that name - with certain modifications - would be continuously used as the name of the main settlement in the region (Scupi-Skopje-Ushkup). Archaeological excavations have proved that this campus was located in the northeastern part of present-day Skopje - under Zajcev Rid, close to where Lepenec River empties into the Vardar.

During the period between the 5th and the 7th centuries, the Balkans and the Skopje region within it was flooded by surges of barbarian people from Middle and East Europe (Goths, Huns, Slavs, Avars, and others). According to written records, in 518 this part of the Balkans faced a disastrous earthquake that heavily damaged the city of Scupi, too. During the Middle Ages, the city of Skopje was to grow on the hill now known as Kale, on the foundations of the previously mentioned Metal and Classical Era settlements. As well as the whole of Macedonia, this region was also under frequent sieges by the Byzantine, Bulgarian, and Serbian state during the whole period of the Middle Ages.

Macedonian feudal kings (Tsar Samoil, Kings Volkasin and Marko) also reigned in this most important city center of the Balkans (among other things, the seat of Serbian Tsar Dusan).

Towards the end of the 14th century, after Skopje became part of the Ottoman Empire, most Christian temples were demolished. On the other hand, however, village churches and monasteries located on the hills surrounding Skopje were preserved. They may be visited even today as part of the authentic natural environs: St. Pantelejmon in Gorno Nerezi (12th century), St. Dimitrija in Susica (14th century), etc. During the Turkish period, Skopje remained an important military, political, trading, and craftsmanship centre of the central Balkans, which was now within the Ottoman Empire. Also, there were Turkish baths, inns (guesthouses), and bezistens.

In 1689, during the Austro-Hungarian war, Austrian General Picollomini set the city on fire. After the fire, many Turkish buildings were reconstructed and have remained until the present day, adding to the charm of the Old Bazaar.

In the 18th and the 19th centuries the Christian population started moving back to Skopje from the surrounding Macedonian regions. Due to the north-south railroad, the city was linked with other regions in Europe.

After World War I, Skopje became part of Serbia and later of the first Yugoslav Federation. Skopje was proclaimed the capital of Macedonia. The disastrous earthquake interrupted the fast development of the city in 1963. But soon afterwards it was completely rebuilt with the assistance of the whole Yugoslav and world community, showing their solidarity with the people of Skopje. Sadly, the old architecture was not restored, but new and modern buildings were built instead. After the breakup of the Yugoslav Federation, in 1991, Skopje remained the capital of the newly independent Republic of Macedonia.

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