Small animal functional magnetic resonance imaging has great potential in a range of basic neuroscientific applications. To maintain stable experimental conditions, animals are usually anesthetized during acquisition. However, anesthesia regimes influence neural activity through their influence on neurovascular coupling. To investigate these mechanisms, we compared the BOLD response following hypercapnia in mice anesthetized under isoflurane or dexmedetomidine. We found that the impact of hypercapnia is much more potent in animals anesthetized under dexmedetomidine, but that FC is much stronger under isoflurane, suggesting that this response does not predict a more pronounced reduction in FC as a consequence of anesthesia.