Windows were shattered and cracks appeared in walls when the quake struck, at a depth of around 10km, just two kilometres to the north-easy of the city.
Photos posted on social media show minor damage, including shattered roof tiles, and spooked residents gathered outside their homes.
Shop floors were also covered in items as the quake caused shelves to sway or collapse.
A witness said: “People ran out on to the street in a panic.”
Skopje was almost completely destroyed by an earthquake in 1963, which killed over 1,000 people in what was one of Europe’s worst-ever natural disasters.
The earthquake this afternoon could also be felt in neighbouring Kosovo.