Aerobic exercise is well recognized to be beneficial to physical and mental health. Many studies have shown that aerobic exercise can improve the human immune system, but whether it could affect lung regeneration and inflammation remained unclear. Bronchioloalveolar stem cells (BASCs) play a key role in lung regeneration and repair, but it is unclear whether aerobic exercise affects BASCs. Here, we randomly divided 8 weeks old male mice into three groups: the control group without any aerobic exercise; the rest group which received 2 weeks of aerobic exercise (running wheel training) plus 5 days’ rest, and the exercise group which received 2 weeks of aerobic exercise without any rest. Our data indicated that mice in the exercise group had significantly increased BASCs compared to the control group, such difference did not exist in the rest group. Furthermore, the immune profiling suggested that lung inflammation was slightly up-regulated in the exercise group, particularly the inflammatory monocytes and IL-17A+ T cells. In conclusion, we provide direct evidence showing that aerobic exercise can facilitate lung regeneration with mild inflammatory effect, this finding is of great importance in the current COVID-19 pandemic.