Stem cell transplantation is a promising method in the treatment of spinal cord injury (SCI). Researches have shown that stem cell-derived exosomes as well as its contents such as microRNAs contribute to the protective effects of stem cell against SCI. However, the effects of exosomes derived from bone marrow stem cells on SCI and the underlying mechanisms remain unknown. In this study, we collected bone marrow stem cells derived exosomes (BMSCs-exo) to deal with SCI rats and LPS induced microglia to explore the possible mechanisms. We found that BMSCs-exo showed significant effects on decreasing pro-inflammatory cytokines as well as increasing Basso–Beattie–Bresnahan score after acute SCI. MicroRNA-181c levels in tissue were elevated with the use of BMSCs-exo. Then we verified the effect in vitro and found that in LPS induced microglia, the administration of BMSCs-exo could inhibit the expression of pro-inflammatory cytokines, and the phosphorylation of NF-κB signal was also suppressed. During which, the expression of microRNA-181c in microglia was elevated. When LPS induced microglia were treated with BMSCs-exo over-expressing microRNA-181c, the levels of pro-inflammatory cytokines decreased. Then bioinformatics techniques were used to detect the possible target gene of microRNA-181c and then PTEN was found as a candidate. Further experiments showed that the protection effects of BMSCs-exo over-expressing microRNA-181c could be antagonized by the elevation of PTEN expression both in vitro and in vivo. In conclusion, we verified that BMSCs-exo could protect against SCI through its content microRNA-181c which suppressed the inflammation in microglia and spinal cord. It was related to the inhibition of PTEN and the suppression of NF-κB signal, and finally decreasing inflammation and apoptosis in spinal cord and improved SCI.