Bone marrow-derived mesenchymal stem cells (BMSCs) have the potential to be used for the treatment of delayed union, nonunion or persistent bone defects in MSC-based cell therapy. However, implantation of BMSCs into the fracture site is confronted with apoptosis on account of harsh conditions and oxidative stress. In the present study, the anti-apoptotic effects of berberine (BBR) on BMSCs subjected to hydrogen peroxide (H2O2) are investigated, and the potential underlying mechanisms are explored. Oxidative injury was induced by exposure to H2O2, and cell viability was assessed using a cell counting kit-8 assay. The apoptosis of BMSCs was measured by Hoechst 33258 and Annexin V-fluorescein isothiocyanate/propidium iodide assay. Reactive oxygen species staining and superoxide dismutase (SOD) assay were applied to assess the anti-oxidative effect of BBR. Finally, western blot was performed to measure the expression levels of phosphorylated (p)-Akt, B-cell lymphoma 2 (Bcl-2), Bcl-2-associated X protein (Bax) and cleaved caspase-3. In the present study, it was identified that BBR remarkably attenuated H2O2-induced apoptotic cell death via quenching ROS production and increasing SOD activity. Further studies indicated that BBR can reduce apoptosis by upregulating the expression level of p-Akt and Bcl-2, and downregulating the expression levels of Bax and cleaved caspase-3. Taken together, the results of the present study demonstrate that pretreatment with BBR could alleviate H2O2-induced apoptosis in rat BMSCs in vitro.