Current decellularization methods for articular cartilages require many steps, various and high amounts of detergents, and a relatively long time to produce decellularized scaffolds. In addition, such methods often damage the essential components and the structure of the tissue. This study aims to introduce a novel perfusion-based bioreactor (PBB) method to decellularize bovine articular cartilages efficiently while reducing the harmful physical and chemical steps as well as the duration of the process. This leads to better preservation of the structure and the essential components of the native tissue. Firstly, a certain number of channels (Ø 180 μm) were introduced into both sides of cylindrical articular bovine cartilage disks (5 mm in diameter and 1 mm in thickness). Next, the disks were decellularized in the PBB and a shaker as the control. Using the PBB method resulted in ∼90% reduction of DNA content in the specimens, which was significantly higher than those of the shaker results with ∼60%. Also, ∼50% sulfated glycosaminoglycan (sGAG) content and ∼92% of the compression properties were maintained implying the efficient preservation of the structure and components of the scaffolds. Moreover, the current study indicated that the PBB specimens supported the adherence and proliferation of the new cells effectively. In conclusion, the results show that the use of PBB method increases the efficiency of producing decellularized cartilage scaffolds with a better maintenance of essential components and structure, while reducing the chemicals and steps required for the process. This will pave the way for producing close-to-natural scaffolds for cartilage tissue engineering.