Background The European roe deer (Capreolus capreolus) is a species particularly reactive to all kinds of negative stimuli. Hunting activity is one of the most potent stressors that disturbs the welfare of wild animals. During stress, various endocrine responses are elicited to improve the physical performance of the affected individual. A commonly assessed hormone for overcoming stressful situations is cortisol (CORT). In this study, plasma CORT levels in roe deer were assessed during the season of the most intense stalking hunts in Poland (summer vs. late autumn), the sex of the harvested animals (males vs. females), and age of harvest animal. In addition, the health status of the roe doe was evaluated on the basis of selected indices of blood chemistry, which could be associated with circulating cortisol levels. Results The mean cortisol levels were 58.066 ng/ml in the male group (summer) and 27.694 ng/ml in the female group (late autumn). Higher CORT levels were associated with a significantly lower of total cholesterol, lactate dehydrogenase, and uric acid (p < 0.05). Moreover, the mean concentration of uric acid was negatively correlated with the level of CORT in the male and female groups (p < 0.05). Together with the increase in mean CORT level, the HDL cholesterol of all the tested animals increased significantly (p < 0.05). Conclusions Higher CORT in males during the summer than in females during the late autumn were most likely due to the arousal with the mating season. The level of CORT increased with the animals’ age. Uric acid and age are both predictors of roe deer’s serum CORT level.