Stem cell therapy is considered an important and innovative tool for applied research in andrology, especially in infertility; therefore, it was later adapted as potential therapeutic agents. This study aimed to evaluate rat mononuclear bone marrow cells' ability to recover testis cells in cyclophosphamide (CTX)-treated rats and to assess its effects on hormonal and histopathological changes. The bone marrow cells were harvested from femurs and tibias of rats and purified by a Histopaque gradient. Mononuclear bone marrow cells transplantation was performed by intravenous injection of cells in cyclophosphamide-treated animals. Three weeks after transplantation, blood samples were collected and analyzed for hormonal assay. In addition, the testes were collected for histological and histopathological determination. The results depicted that the serum levels of all tested hormones were significantly different among the three experimental groups G1 (control, healthy animals), G2 (CTX induced infertility and untreated) and G3 (CTX induced infertility and treated with stem cells). FSH and LH levels were significantly increased in G2 (CTX) compared to G1 and G3. Total and free testosterone levels were slightly higher in G3 compared to G2. Mononuclear bone marrow cell transplantation promoted cellular reorganization of the seminiferous epithelium. Also, spermatogenesis regeneration was improved. In conclusion, bone marrow stem cells can regenerate the damaged testicular elements and hence restore hormonal regulation in cyclophosphamide treated rat. Therefore, the treatment of male infertility and testosterone deficiency could be therapeutically treated by using stem cells.