This study investigated the effect of blood CO2 levels on brain activity from a number of perspectives. We first showed that hypercapnia reduced metabolic activity in the brain. Second, neural activity was assessed indirectly by BOLD fcMRI and the data suggested that CO2 inhalation caused a decrease in spontaneous brain connectivity. Finally, EEG was used as a direct measure of neural activity and the results showed that hypercapnia caused a relative increase in lower frequency power spectra. Overall, our data showed a suppressive effect of CO2 on brain activity.