We present the first demonstration of chronic in vivo imaging of microglia in mice undergoing voluntary wheel running. We find that healthy mice undergoing voluntary wheel running have similar microglia dynamics, morphologies, and responses to injury when compared to sedentary mice. This suggests that exercise over a period of 1 mo does not grossly alter cortical microglial phenotypes and that exercise may exert its beneficial effects on the brain through other mechanisms. Future work examining how microglia dynamics may be altered during exercise in disease or injury models could provide further insights into the therapeutic benefit of exercise. We demonstrate the first use of chronic in vivo imaging of microglia over time during physical exercise. We found that microglia movement, morphology, and process motility were remarkably stable during voluntary wheel running (VWR). Additionally, microglia in running mice respond similarly to laser ablation injury compared to sedentary mice. These findings indicate that VWR does not induce changes in microglia dynamics in healthy adults. Exercise may elicit positive effects on the brain through other mechanisms.