This study aimed to explore how amelogenin can improve stem cells from human exfoliated deciduous teeth (SHED)-based bone regeneration and promote tissue healing as a treatment for critical-sized bone defects. SHED was induced into bone differentiation by using osteogenic differentiation medium. Real-time polymerase chain reaction, alkaline phosphatase (ALP) staining and quantification, and Alizarin Red S staining, as well as calcium and osteocalcin quantification were performed to assess differentiation. On day 18, a significant increase was observed in the expression of , , , , , , , , and . Osteocalcin gene expression continued to increase significantly. ALP activity was significantly higher in the amelogenin-treated group than in the control group on days 7, 10, and 14. On day 14, enhanced ALP staining was observed in the amelogenin-treated group. Calcium and osteocalcin levels were significantly higher in the amelogenin-treated group than in the control group on day 21. This study suggests that combining SHED and amelogenin may be effective for bone regeneration, offering a potential new approach in regenerative medicine.