There is very little about the impact that sports training has on female football referees. Therefore, we determined the effects of a 40-week physical preparation, including a full football season, on plasma testosterone and cortisol concentrations and physical performance in female football referees. Plasma cortisol and testosterone concentrations were assayed together with fitness tests at the beginning of the training period (T0, in September), after 8 weeks from T0 (T1), at the mid of the season (T2, 24 weeks after T0), and at the end of the season (T3, in June, 40 weeks after T0). Plasma cortisol increased during the first period and up to T2 (from 15.4 ± 4.7 to 28.5 ± 3.9 µg/dl; p < 0.001), and then decreased at the end of the season (T3: 16.0 ± 2.4 µg/dl). Plasma testosterone concentration in T0 was 14.2±0.37 µg/dl and increased in T1 (57.1 ± 3.7 µg/dl) and T2 (47 ± 3.7 µg/dl) and then decreased in T3 (33.5 ± 2.8 µg/dl). Resting testosterone levels in women were very low (14,2 ± 0.37 µg/dl) (Figure 3c). Testosterone increased in T1 (57.1 ± 3.7 µg/dl) and T2 (47 ± 3.7 µg/dl) whilst, at the end of the season, its concentration decreased (33.5 ± 2.8 µg/dl) (Figure 3c). Significant improvements were observed in all physical performances during the observed period (ANOVA, p < 0.05). Finally, testosterone and cortisol concentrations significantly (p < 0.0001 for both) correlated with maximal oxygen consumption. In T1, testosterone concentration was also significantly correlated with running speed test (p < 0.001). In conclusion, training induces endocrine changes in order to maintain body homeostasis in women referees. It is important that coaches and sports scientists regularly observe changes in endocrine function induced by training and matches in female referees, because they can help maximize referees' performance and limit cases of overtraining.