Carbon dioxide (CO ₂ ), the major product of metabolism, has a strong impact on cerebral blood vessels, a phenomenon known as cerebrovascular reactivity. Several vascular risk factors such as hypertension or diabetes dampen this response, making cerebrovascular reactivity a useful diagnostic marker for incipient vascular pathology, but its functional relevance, if any, is still unclear. Here, we found that GPR4, an endothelial H ⁺ receptor, and endothelial Gα _q/11 proteins mediate the CO ₂ /H ⁺ effect on cerebrovascular reactivity in mice. CO ₂ /H ⁺ leads to constriction of vessels in the brainstem area that controls respiration. The consequential washout of CO ₂ , if cerebrovascular reactivity is impaired, reduces respiration. In contrast, CO ₂ dilates vessels in other brain areas such as the amygdala. Hence, an impaired cerebrovascular reactivity amplifies the CO ₂ effect on anxiety. Even at atmospheric CO ₂ concentrations, impaired cerebrovascular reactivity caused longer apneic episodes and more anxiety, indicating that cerebrovascular reactivity is essential for normal brain function. The site-specific reactivity of vessels to CO ₂ is reflected by regional differences in their gene expression and the release of vasoactive factors from endothelial cells. Our data suggest the central nervous system (CNS) endothelium as a target to treat respiratory and affective disorders associated with vascular diseases.