Cerebral hypoperfusion impairs brain activity and leads to cognitive impairment. Left and right common carotid arteries (CCA) are the major source of cerebral blood supply. It remains unclear whether blood flow in both CCA contributes equally to brain activity. Here, CCA blood flow was evaluated using ultrasonography in 23 patients with cerebrovascular diseases. Resting-state brain activity and cognitive status were also assessed using magnetoencephalography and a cognitive subscale of the Functional Independence Measure, respectively, to explore the relationships between blood flow, functional brain activity, and cognitive status. Our findings indicated that there was an association between blood flow and resting-state brain activity, and between resting-state brain activity and cognitive status. However, blood flow was not significantly associated with cognitive status directly. Furthermore, blood velocity in the right CCA correlated with resting-state brain activity, but not with the resistance index. In contrast, the resistance index in the left CCA correlated with resting-state brain activity, but not with blood velocity. Our findings suggest that hypoperfusion is important in the right CCA, whereas cerebral microcirculation is important in the left CCA for brain activity. Hence, this asymmetry should be considered when designing appropriate therapeutic strategies.