The carbon balance processes of plants in response to diurnal environmental changes are critical for their growth and survival. While sex-specific responses in photosynthesis to environmental stress have been observed in several dioecious plant species, the diurnal dynamics of carbon balance in male and female individuals remain unexplored. Here, we investigated the diurnal variations of photosynthetic rate (A), dark respiration rate (R_d), A/R_d, and the concentration, pool, and allocation of nonstructural carbohydrates (NSC) of male and female mulberry (Morus alba) seedlings. Males exhibited the highest A at 09:00, while females had the highest A and R_d at 13:00. Male A was higher than female A at 09:00, whereas male R_d was lower than female R_d at 13:00. The A/R_d was higher in males than in females. The peak of NSC concentration in males was earlier than in females, and the NSC concentration and storage in the whole plant, leaves and bark were generally higher in males than in females across most time points. The average NSC allocation followed the leaves > roots > bark ≈ trunk trend, but its dynamic changes over the daily cycle were more pronounced in females than in males. These findings suggest that carbon balance processes in mulberry seedlings exhibit sex-specific responses to diurnal changes, with females displaying greater sensitivity to these variations. This study provides the first attempt to explore such responses in woody plants and suggests that future carbon cycle models for terrestrial plants should incorporate plant sex.