Capillary flow patterns are highly heterogeneous in the resting brain. During hyperemia, capillary transit-time heterogeneity (CTH) decreases, in proportion to blood's mean transit time (MTT) in passive, compliant microvascular networks. Previously, we found that functional activation reduces the CTH:MTT ratio, suggesting that additional homogenization takes place through active neurocapillary coupling mechanisms. Here, we examine changes in the CTH:MTT ratio during hypercapnic hyperemia in anesthetized mice (C57Bl/6NTac), expecting that homogenization is smaller than during functional hyperemia. We used an indicator-dilution technique and multiple capillary scans by two-photon microscopy to estimate CTH and MTT. During hypercapnia, MTT and CTH decreased as derived from indicator-dilution between artery and vein, as well as between arterioles and venules. The CTH:MTT ratio, however, increased. The same tendency was observed in the estimates from capillary scans. The parallel reductions of MTT and CTH are consistent with previous data. We speculate that the relative increase in CTH compared to MTT during hypercapnia represents either or both capillary constrictions and blood passage through functional thoroughfare channels. Intriguingly, hemodynamic responses to hypercapnia declined with cortical depth, opposite previous reports of hemodynamic responses to functional activation. Our findings support the role of CTH in cerebral flow-metabolism coupling during hyperemia.