Cordyceps species have been traditionally used as for the enhancement of sexual function, but its direct evidence is lacking. We investigated the spermatogenic effect of Cordyceps militaris (CM) as supplementation with CM mycelium to 7-week-old male Sprague-Dawley (SD) rats. Ninety rats (30 for each group) were selected to regular diet or diet supplemented with CM mycelium (1% and 5%) for 6 weeks. Epididymal sperm were collected from 6 animals per group at each interval of observation. They were allowed to recover for one week. The quality and quantity of sperm were compared in these rats. The CM supplementation resulted in an increase of serum cordycepin concentration (n = 6, each group) that correlated with treatment time and the cordycepin level was significantly higher (p < 0.05) in 5% group as compared to 1% group at the 5th and 6th week. Epididymal sperm count was enhanced significantly from the control, at the 5th week and peaked at the 6th week in both groups supplemented with CM (each time point, n = 6; p < 0.05) and maintained for 2 weeks after stopping the treatment. Increased serum testosterone and estradiol-17 (E2) concentrations were found in rats with the CM supplementation (p < 0.05), but not other hormones such as follicle stimulating hormone (FSH), luteinizing hormone (LH) or prolactin. Importantly, percentages of motile sperm cells were also enhanced significantly (p < 0.05) paralleled the serum testosterone pattern from the supplement groups as compared to the control group. Taken together, these results indicate that supplementation with CM improves sperm quality and quantity in rats.