The proper function of the hypothalamic-pituitary-ovarian axis is essential for maintaining proper female reproductive function. In female mammals, the hypothalamic-pituitary-ovarian axis regulates reproductive changes that take place in the estrus cycle and are necessary for successful reproduction. This study aimed to investigate the influence of thymus gland on the female reproductive function in different stages of life. This present study was conducted to investigate the effect of thymectomy on the estrus cycle in prepubertal (5th week) and pubertal (7th week) thymectomized guinea pigs. In this study, 24 female guinea pigs, six thymectomized and six sham-operated in each group were studied. Gonadotropin and 17β-estradiol levels were assessed at regular intervals (days 0, 3, 6, 9, 12 and 15) of the estrus cycle, and the length of the oestrous cycle in the thymectomized and sham-operated guinea pigs was determined. The results showed no significant difference in gonadotropin and 17β-estradiol were detected in thymectomized versus sham-operated guinea pigs at any intervals of the oestrous cycle. Thymectomy did not affect the length of the oestrous cycle of females. In conclusion, the present study results suggested that the presence of thymus during prepubertal and pubertal life was not necessary to regulate the oestrous cycle of female guinea pigs.