Bone blocks are proposed in oral bone regeneration for their biocompatibility and osteoconductivity. Human dental pulp stem cells (hDPSCs) have been used with bone substitutes as a biocomplex. Melatonin, produced by the pineal gland, has specific functions in the oral cavity in bone remodeling and enhancing the dual actions on osteoblasts and osteoclasts, the genic expression of bone markers. This study evaluated the osteogenic differentiation of hDPSCs, stimulated by melatonin on equine bone blocks. hDPSCs were cultured in growth medium (GM) or differentiation medium (DM) with or without the presence of equine bone blocks and 100 μm melatonin. After 7, 14, and 21 days of culture, expression of miRNAs (miR-133a, miR-133b, miR-135a, miR-29b, miR-206, and miR- let-7b) and genes (RUNX2, SMAD5, HDAC4, COL4a2, and COL5a3), osteocalcin levels and histolgic analyses were evaluated. Melatonin and equine blocks increased the osteogenic potential of hDPSCs even in GM, regulated miRNA and gene expression related to osteogenesis, and increased osteocalcin. hDPSCs cultured in DM showed a significantly higher osteogenic potential compared to GM. This study suggests that equine bone blocks and melatonin enhanced osteogenesis, stimulating early stages of cell differentiation. hDPSCs/equine bone block and melatonin represent a promising, useful biocomplex in bone regeneration with a potential for a possible clinical application.