Cerebral blood velocity (CBv) increases in response to moderate exercise in humans, but the magnitude of change is smaller in children compared to post-pubertal adolescents and adults. Whether sex differences exist in the anterior or posterior CBv response to exercise across pubertal development remains to be determined. We assessed middle cerebral artery (MCAv) and posterior cerebral artery (PCAv) blood velocity via transcranial Doppler in 38 pre-pubertal (18 male) and 48 post-pubertal (23 male) with cerebrovascular and cardiorespiratory measures compared at baseline and ventilatory threshold. At baseline, MCAv was higher in both sexes pre- vs. post-puberty. Females demonstrated a greater MCAv (<i>P</i><0.001) than their male counterparts (pre-pubertal females; 78 ± 11cm.s^-1 vs. pre-pubertal males; 72 ± 8cm.s^-1, and post- pubertal females; 68 ± 10cm.s^-1 vs. post- pubertal males; 62 ± 7cm.s^-1). During exercise, MCAv remained higher in post-pubertal females vs. males (81 ± 15 cm.s^-1 vs. 73 ± 11 cm.s^-1), but there were no differences pre-puberty. The relative increase in PCAv was greater in post- vs pre-pubertal females (51 ± 9cm.s^-1 vs. 45 ± 11cm.s^-1; <i>P</i>=0.032), but was similar in males and females. Our findings suggest biological sex alters anterior cerebral blood velocities at rest in both pre- and post-pubertal youth, but the response to submaximal exercise is only influenced by sex post-puberty.