Their bodies were found before 8:30 local time (06:30 GMT) on Sunday, an official said. Six people are still missing.
Some of the victims drowned in their cars. Parts of the city’s ring road have been swept away in the floods, dragging cars into nearby fields.
Three and a half inches (9.3cm) of rain fell in the capital during the storm.
The Mayor of Skopje, Kove Trajanovski, said: “This is a disaster. We have never experienced such a thing.”
Local media reported that ambulances were called out 65 times across Skopje, more than 20 people were treated in hospital, and the army was called in to help.
Three villages in the north-east of the country were cut off due to landslides.
More rains are forecast for Sunday evening. -BBC