This study aimed to investigate the dose-dependent and time-dependent effect of magnetic iron oxide nanoparticles (MIONPs) on reproduction in male rats. Following their synthesis, the physicochemical properties of MIONPs were determined. Sixty-four adult male rats, aged 90 days were randomly assigned to control (C), orally administered with distilled water, and three treated groups, orally administered with 1, 5, 10 mg/kg/day of MIONPs solution (TL, TM, and TH groups, respectively), for 28 days. Each group was allocated to two subgroups, sacrificed after 14 and 28 days of treatment. After each period, the males were weighed and sacrificed. Decreased body weight and genital organ weights were shown in TM and TH groups, at both experimental periods, compared with control in a dose-dependent manner. The serum concentration of GnRH, FSH, LH, and testosterone increased in the TL group and decreased in TM and TH groups compared with control in a dose-dependent and time-dependent manner. At both periods, the lowest expression levels of pituitary FSHβ and LHβ genes and testicular inh-α and LHR genes were recorded in TM and TH groups, and the highest levels were expressed in the TL group. The testis sections of TL males, showed normal architecture, but those from TM and TH groups showed degenerative and necrotic changes, reduced germinal epithelium, vacuolation, and decreased number of spermatocytes apparent. It is concluded that a low dose of MIONPS has a beneficial effect, whereas moderate or high doses have pathological effects on male reproduction.