Osteoporosis remains a major health challenge due to impaired osteoblast function and reduced bone formation, particularly in glucocorticoid-induced osteoporosis (GIOP). The Wnt/β-catenin signaling pathway plays a critical role in osteogenesis, making it a promising target for protective interventions against osteoporosis-related bone loss. In this study, virtual screening of a natural product library identified Protosappanin B (PB) as a potential Wnt pathway activator with high binding affinity for Wnt receptors. We investigated PB's protective effects on osteoblast function under glucocorticoid exposure using MC3T3-E1 cells treated with dexamethasone (DEX) and an in vivo zebrafish model of GIOP. PB significantly promoted osteoblast proliferation, facilitated cell cycle progression, and attenuated DEX-induced apoptosis in a dose-dependent manner. Additionally, PB enhanced osteoblast differentiation and mineralization, counteracting DEX's inhibitory effects on alkaline phosphatase (ALP) activity and calcium deposition. In zebrafish, PB mitigated DEX-induced skeletal defects, improving bone and craniofacial cartilage formation. Western blot analysis confirmed that PB restored β-catenin levels, activating the Wnt/β-catenin pathway. Notably, the osteogenic effects of PB were abolished by XAV939, a Wnt signaling inhibitor, further supporting its Wnt-dependent mechanism of action. These findings indicate that PB provides protective effects against glucocorticoid-induced osteoblast dysfunction and bone loss by modulating Wnt signaling. This study highlight the potential of PB as a natural agent for preventing GIOP-related bone deterioration and warrants further investigation into its clinical applicability.