Background: Methotrexate (MTX) is an anticancer drug that induces testicular abnormalities but, thyme is antioxidant compound, which scavenges oxidative damage. Objective: this study aimed to investigate the protective role of thyme leave extract on the histological and immunohistochemical testicular changes induced by MTX. Material and Methods: forty adult male rats were used and categorized into 4 equal groups (10 rats/each); Group I:  control rats group without treatment. Group ΙΙ: control rats administrated thyme only for a month, Group ΙΙΙ: rats injected (i.p) with MTX for four weeks, Group ΙV: rats injected with MTX and administrated thyme extract. Results: the control rat testes stained with H&E showed normal histological structure of testes; rats administrated thyme demonstrated   normal structure similar to the normal control.  Rats injected with MTX showed damaged testicular tissue but, rats co-treated with MTX and thyme demonstrated improvement in the testicular structure. The caspase-3 immunostain was expressed in the control and the thyme group as weak reaction in the spermatogonic cells. However, MTX group showed dense reaction for caspase-3 and group of MTX and thyme detected obviously reduction of caspase -3. Normal intense immunoreactive of PCNA was realized in the control and thyme groups. But, MTX group showed an obvious decrement of immunoreactivity and MTX and thyme group expressed more reduction in the immunoreactivity. Conclusion: thyme extract had the ability to ameliorate  the  abnormalities occurred in the testes of rats after MTX treatment.