The authors aimed to evaluate the effects of physical exercise on the metabolism and progression of periodontal disease (PD), induced by ligature in diabetic rats induced by high fat diet and streptozotocin (HFD/STZ). Diabetes Mellitus (DM) was induced by four weeks of a hyperlipidic diet associated with a single low-dose of streptozotocin (35 mg/kg/animal). The exercise groups swam for 60 min/day for eight weeks (five times/week). In the last two weeks of exercise, a ligature was placed around the right and left mandibular first molars. The authors determined alveolar bone loss by morphometry. Blood biochemical profile and serum levels of IL-10 and TNF-α were evaluated by colorimetric and enzyme-linked immunosorbent assays (ELISA), respectively. The diabetic animals subjected to exercise showed decreased alveolar bone loss, lower glycemia, triacylglycerols and glycosylated hemoglobin levels than the controls. Total cholesterol and its fractions (High density lipoprotein—HDL-c, Low density lipoprotein—LDL-c and Very low density lipoprotein—VLDL-c) remained similar among the groups. Animals with PD showed higher levels of TNF-α and lower levels of IL-10, when compared to animals without PD. In diabetic animals with PD, physical exercise decreased TNF-α levels and increased IL-10 levels as well as the IL10/TNF-α ratio. In conclusion, eight weeks of physical exercise improved glycemic control and systemic inflammatory profile, and attenuated alveolar bone loss in rats with DM and PD.