After completing his formation, Ljubenović made his senior debuts with the Romantičari in the 2000–01 First League of FR Yugoslavia.

In the 2006 winter transfer window, Ljubenović moved to Ukraine and signed with Kryvbas Kryvyi Rih.

Over the next five and a half years, Ljubenović played regularly for the side and recorded near 200 appearances in all competitions.

He left the club midway through the 2011–12 season, eventually joining another Premier League side, Oleksandriya.

[1] In July 2018 Zorya's general director Serhiy Rafailov announced that Ljubenović will work in the club as scout in Balkan region.