Bone morphogenetic protein two (BMP-2) has been widely used as an osteoinductive agent in the treatment of bone diseases. However, some side effects, such as osteoclast activation have emerged when it was used at high doses. In this study, by considering the osteoclast-suppressing capability of melatonin (MEL), its effect on osteoclast differentiation induced by BMP-2 was investigated. These two factors, MEL and BMP-2, were embedded into chitosan/hydroxyapatite (HAp) scaffolds that were characterized morphologically by scanning electron microscopy (SEM) and micro-computed tomography (mu-CT). Release profiles of MEL and BMP-2 from scaffolds were determined in vitro and then, the differentiation of RAW 264.7 cells to osteoclasts was investigated on the scaffolds. Results of tartrate-resistant acid phosphatase (TRAP) staining, SEM imaging and expression of cathepsin K gene showed that, in the presence of BMP-2, osteoclast differentiation increased, whereas it decreased in MEL and MEL/BMP-2 embedded scaffolds suggesting that melatonin successfully attenuated osteoclast differentiation induced by BMP-2. Thus, the MEL/BMP-2 loaded chitosan/HAp scaffolds that have dual function in enhancing bone formation and inhibiting osteoclast activity are recommended biomaterials in the field of bone regeneration.