Testis ischaemia-reperfusion (I/R) plays a vital role in male infertility. Recent studies have demonstrated that paracrine factors of mesenchymal stem cells exert the transplanted cells' reparative effects. The present experimental study aimed to investigate the effects of conditioned medium (CM) of bone marrow-derived mesenchymal stem cells (BMMSCs). In this study, 21 rats were separated into three groups of 7 animals: sham, I/R and I/R plus CM. Sperm parameters were measured at the end of this study. Moreover, histological parameters were examined. 2-Deoxyuridine 5-triphosphate nick-end labelling (TUNEL) assay was done to assess the apoptotic cells. The count of adhered neutrophils was measured in subtunical venules. Testicular I/R led to a significant reduction in the viability and concentration of sperm and resulted in a significant elevation in the rate of abnormal sperms in comparison with sham. The CM-treated group demonstrated a significant reduction in the rate of abnormal sperm and a significant elevation in the viability and concentration of sperm compared with the I/R group. Based on the morphometric analysis, in the I/R group, epithelial thickness and seminiferous tubule diameter significantly decreased in comparison with sham. A significant reduction was seen between the I/R and sham groups regarding the mean testicular biopsy score (MTBS) value. However, an improvement was observed in the I/R + CM group MTBS value in comparison with the I/R group. TUNEL assay showed that the apoptotic cells in the seminiferous tubules belonging to the I/R group were significantly higher compared with the control. Nevertheless, apoptotic cells were reduced in the I/R + CM group compared with the I/R group. Results of the present study showed that CM of BMMSCs exerts protective effects on the testicular I/R damages.