Aim Post-traumatic stress disorder (PTSD) requires more effective treatment options with fewer side effects. Stem cell therapy, as a novel approach, has been investigated in the treatment of various diseases, including brain disorders. This study investigated the effects of bone marrow stromal cells (BMSCs) and the combination of BMSCs with exercise on corticosterone, BDNF and IGF-1, and anxiety-like behaviors in a male rat model of PTSD. Methods Male adult Wistar rats were subjected to PTSD induced by the single prolonged stress (SPS) model. 7 days after SPS, BMSCs were injected intravenously. The exercise started on day 11 and continued for 4 weeks. On day 40th, anxiety behavior, corticosterone, BDNF, and IGF-1 were tested. P < 0.05 was considered as a significant level. Results The study showed that a combination of BMSCs and exercise significantly reduced anxiety-related behaviors, and alterations in BDNF, IGF-1, and corticosterone levels. Also, BMSCs alone significantly reduced some of the PTSD-induced impairments. However, exercise alone showed greater efficiency in comparison with BMSCs alone. Conclusion According to the results, although combination therapy effectively improved PTSD-related complications, exercise had relatively comparable effects on PTSD. Exercise has the potential to enhance the efficacy of BMSC therapy. Further research is required to determine whether BMSC therapy is sufficiently efficacious and safe in clinical settings.