One of the main cause of male infertility is non-obstructive azoospermia, which is not manageable medically. The first aim of the current research was to show the effect of extracellular vesicle-contained conditioned media (CM) instead of mesenchymal stromal/stem cells (MSCs) for treatment of non-obstructive azoospermia. In the next step, we aimed to study the differentiation potential of MSCs into spermatocytes after injection of MSCs in mice seminiferous tubules. This study has provided an applied treatment for busulfan-induced azoospermia using adipose tissue-derived (AT-MSCs) and bone marrow-derived MSCs (BM-MSCs) and bone marrow CM (BMCM) in animal models. In this regard, 30 male adult Balb/C mice (30±5g) and two female eGFP+/+ Balb/C mice (30±5g) were used to design experimental groups and to culture stem cells, respectively. Then, six groups including intact control, azoospermia, AT-MSC therapy, BM-MSC therapy, BMCM therapy, and spontaneous healing groups were considered. All groups except intact control were induced azoospermia by injecting two doses of busulfan (10 mg/kg) with 21 days’ interval. Testes of all mice were removed and studied through histomorphometry and flow cytometry analysis 60 days after treatment. Histomorphometry and flow cytometry evaluation of testes showed normal morphology of most of the seminiferous tubules of therapy groups as well as successful recovery of spermatogenesis, but spermatogenesis was not observed in the azoospermia group. It is worth notable that the results of the BM-MSC therapy group were more favorable than other therapy groups. Consequently, AT-MSC, BM-MSC and BMCM can be strongly suggested as candidates in the therapy of azoospermia.