Founded in 588 BC by Greeks from Corinth, the city quickly grew to 50,000 residents by the second century BC. Apollonia later became a free Roman city after it sided with Julius Caesar during the war against Pompey. It developed into a cultural center of the arts until the 3rd century AD when an earthquake rerouted a river and lead to the city's decline.

The Austrians started escavating the site during W.W.I and the French later continued the work through the 1920s and 30s. While Albanian archaeologists have made some progress over the last few decades, much of this ancient city still remains buried in the hill.