Decreased cerebrovascular blood flow and function are associated with lower cognitive functioning and increased risk of neurodegenerative diseases. Prolonged sitting impairs peripheral blood flow and function, but its effects on the cerebrovasculature are unknown. This study explored the effect of uninterrupted sitting and breaking up sitting time on cerebrovascular blood flow and function of healthy desk workers. Fifteen participants (10 male, 35.8 ± 10.2 yr, body mass index: 25.5 ± 3.2 kg/m2) completed, on separate days, three 4-h conditions in a randomized order: 1) uninterrupted sitting (SIT), 2) sitting with 2-min light-intensity walking breaks every 30 min (2WALK), or 3) sitting with 8-min light-intensity walking breaks every 2 h (8WALK). At baseline and 4 h, middle cerebral artery blood flow velocity (MCAv) and CO2 reactivity (CVR) of the MCA and carotid artery were measured using transcranial Doppler (TCD) and duplex ultrasound, respectively. Cerebral autoregulation (CA) was assessed with TCD using a squat-stand protocol and analyzed to generate values of gain and phase in the very low, low, and high frequencies. There was a significant decline in SIT MCAv (-3.2 ± 1.2 cm/s) compared with 2WALK (0.6 ± 1.5 cm/s, P = 0.02) but not between SIT and 8WALK (-1.2 ± 1.0 cm/s, P = 0.14). For CA, the change in 2WALK very low frequency phase (4.47 ± 4.07 degrees) was significantly greater than SIT (-3.38 ± 2.82 degrees, P = 0.02). There was no significant change in MCA or carotid artery CVR ( P > 0.05). Results indicate that prolonged uninterrupted sitting in healthy desk workers reduces cerebral blood flow; however, this is offset when frequent short-duration walking breaks are incorporated. NEW & NOTEWORTHY Prolonged uninterrupted sitting in healthy desk workers reduces cerebral blood flow. However, this reduction in cerebral blood flow is offset when frequent short-duration walking breaks are incorporated into this sitting period. For those who engage in long periods of sedentary behavior, chronically breaking up these sitting periods with frequent active break strategies may have important implications for cerebrovascular health; however, further research should explore this hypothesis.