A major feature of chronic periodontitis (CP) is the damage and destruction of alveolar bone. Periodontal ligament stem cells (PDLSCs) can differentiate into bone and improve CP. Exendin-4 (Ex-4) has been shown to have anti-inflammatory mechanisms and can promote bone regeneration. However, the effects of Ex-4 on the osteogenic differentiation of PDLSCs in the inflammatory microenvironment remains uncharacterized. In this study, we assessed the effects of Ex-4 on PDLSCs stimulated with lipopolysaccharide (LPS) to mimic the inflammatory environment. PDLSCs proliferation was assessed through CCK-8 assays and osteogenic differentiation was measured using Alizarin Red staining. The anti-inflammatory and osteogenic mechanisms of Ex-4 were assessed by western blot, RT-PCR, ELISA and immunofluorescence. We found that LPS treatment promoted the proliferative capacity of PDLSCs and inhibited their osteogenic differentiation. However, Ex-4 reversed these effects through suppressing PDLSCs proliferation and promoting osteogenic differentiation. Ex-4 increased Runx2, ALP, and Osx levels and decreased TNF-α and IL-6 expression. Ex-4 also reduced the expression of IκBα and p-IκBα, and inhibited the nuclear translocation of NF-κB/p65. The expression of β-catenin decreased in nucleus after co-treatment of Ex-4 with LPS. Taken together, these data demonstrate that Ex-4 promotes PDLSCs osteogenic differentiation in the inflammatory microenvironment through regulating NF-κB and Wnt signaling.