Injectable anesthetics are commonly used in murine experimental procedures. However, these agents may result in neurotoxicity, which should be considered in interpretation of experimental results. We evaluated acute effects of 2 different anesthetic combinations on juvenile mouse brain development using structural MRI to assess impact on the brain. We compared the use of ketamine-xylazine, a commonly used injectable anesthetic combination in mice, to alfaxalone-xylazine in the context of noninvasive procedures requiring immobilization (that is, not a surgical plane of anesthesia). In this longitudinal study, we used MRI to produce three-dimensional scans of mouse brains at 2 time points (postnatal days 14 and 23), analogous to early childhood to prepubescence in humans. At postnatal day 16, mice were either dosed with ketamine-xylazine, alfaxalone-xylazine, or left untreated. From the scans, we quantified whole brain and structure volumes across the brain, comparing growth between time points and modeling the effect of both anesthetics compared with controls. Anesthetic parameters were measured, and general health and welfare were monitored during and after each injectable anesthesia drug condition. Results indicate that systemic and brain toxicity were reduced in mice treated with alfaxalone-xylazine compared with ketamine-xylazine. In addition, both ketamine-xylazine and alfaxalone-xylazine reliably anesthetized all mice, although mice administered ketamine-xylazine showed increased weight loss compared with the alfaxalone-xylazine in the postanesthetic period. These findings highlight alfaxalone-xylazine as a convenient and possibly safer alternative anesthetic for mouse brain development studies when compared with ketamine-xylazine and as a viable option as an injectable anesthetic in juvenile mice.