The Lepenac springs out on the Oshlak mountain, east of the city of Prizren, at an altitude of 1,833 m (6,014 ft).

The Lepenac continues between the Šar Mountains in the south and Nerodimka mountain in the north, next to the villages of Biti e Poshtëme, Gotovushë, Brod and Doganaj, where the river makes an elbow turn to the south, entering the Kosovo field.

Immediately entering the Greater Skopje area, it receives several small streams from the left, from the Skopska Crna Gora mountain.

It passes next to the ruins of the ancient city of Scupi, but has no major settlements on its Macedonian course, before it reaches the northern suburbs of Skopje, Bardovci and Novo Selo, and empties into the Vardar at the Skopje's northern borough of Ǵorče Petrov at an altitude of 262 m (860 ft).

The Lepenac was a part of the artificial bifurcation, as the Nerodime connected both Lepenac and Sitnica rivers via a canal, thus connecting Aegean and Black Sea drainage basins, but the canal was covered after World War II.