Inflammation-related bone defects pose a heavy burden on patients and orthopedic surgeons. Although stem-cell-based bone repair has developed rapidly, it is of great significance to characterize bio-active molecules that facilitate bone regeneration. It is reported that a glucagon-like peptide 1 receptor agonist, exendin-4, promoted bone regeneration mediated by the transplantation of adipose-derived stem cells in a metaphyseal defect mouse model of femur injury. However, the underlying mechanism is unclear. Bone imaging, immunohistochemistry real-time PCR and western blot analysis were used in the present study, and the results revealed that exendin-4 increased the transcription of the osteogenic differentiation-related genes and induced osteogenic differentiation in situ. Furthermore, the present data obtained from sorted adipose-derived stem cells revealed that exendin-4 promoted osteogenic differentiation and inhibited adipogenic differentiation in vitro. These findings indicated that exendin-4 facilitates osteogenic differentiation of transplanted adipose-derived stem cells for bone repair and illuminated clinical prospects of both adipose-derived stem cells and exendin-4 in stem-cell-based bone defect repair.