Rapamycin (mTOR inhibitor) has been reported to have negative effect on human male gonadal function. Previously, we showed that mTOR signalling molecules are expressed during early spermatogenesis in mice. The objective of this study was to investigate the role of mTOR signalling in meiosis both during the first wave of spermatogenesis and also during adult spermatogenesis. Day 5 post-partum mice were administered rapamycin and retinoic acid (RA; a Stra8 activator), and expression of p-p70S6K and Stra8 proteins was evaluated. p-p70S6K and Stra8 protein expressions decreased in post-natal testes after rapamycin treatment. Stra8 protein expression increased after RA and rapamycin+RA administrations in post-natal testes. In adult mice, rapamycin was administrated for 1 or 4 weeks. Morphological analysis for testicular damage and TUNEL assay was performed. After rapamycin administration, germ cell loss increased in adult testes. Ultrastructural analysis revealed disorganised testicular morphology and vacuolisation. The number of apoptotic germ cells increased after 4 weeks rapamycin administration. Stra8 and Dmc1 expressions decreased in 4 weeks rapamycin group, whereas Sycp3 and VASA expression did not change. Our findings suggest that mTOR pathway has an important role in meiotic progress of male germ cells both during first wave of spermatogenesis and in adult mice.