In this study, melatonin/2-hydroxypropyl-β-cyclodextrin (HPβCD) inclusion complex was prepared by using microwave irradiation in a very short time. Phase-solubility studies indicated a linear increase in the solubility of melatonin with HPβCD demonstrating Higuchi’s AL-type phase solubility profiles and the formation of 1:1 stoichiometric inclusion complexes. Also, the ability of inclusion complex formation was promoted at microwave conditions compared to room conditions. The structure of inclusion complex was determined by FTIR, DSC, XRD, 1H NMR and 13C NMR studies. Both of pure melatonin and melatonin/HPβCD inclusion complex were loaded into the chitosan scaffolds that were prepared by freeze-drying method and the effect of released melatonin on human osteosarcoma cells (MG-63) was investigated in vitro. Approximately 9 mM melatonin concentration caused time dependent cell death by reducing the proportion of the cells in the G2/M phase rather than S phase. In conclusion, melatonin/HPβCD inclusion complex loaded chitosan scaffolds could be considered as an alternative system for the human osteosarcoma therapy.