Background It has been reported that exercise could improve diabetes via the VitD-FGF23-sKlotho axis. Objective We evaluated the effects of 8 weeks of endurance and resistance training on serum levels of fibroblast growth factor 23 (FGF23), soluble klotho (s-Klotho), 1,25-dihydroxyvitamin D (VitD), and diabetes biomarkers in overweight/obese postmenopausal type 2 diabetic (T2DM) women. Methods Thirty overweight/obese postmenopausal women with T2DM were randomly divided into three groups, including endurance exercise (3 days/week of walking and jogging), resistance exercise (60 min weight resistance training 3 days/week), and control groups (no physical activity and dietary change). Before and after the 8-week training, serum levels of FGF23, s-Klotho, VitD, blood sugar, lipid profile, and hemoglobin A1c (HbA1c) as well as anthropometric, physiological, and cardiac characteristics were evaluated. Results The endurance or resistance training did not significantly change the anthropometric and cardiac parameters (p > 0.05), and only fat percent, resting heart rate, and systolic blood pressure levels were significantly decreased after the endurance exercise (p < 0.05). Both endurance and training exercises could improve serum levels of insulin and glucose. The serum levels of FGF23 and s-Klotho were significantly increased in the endurance and resistance groups (p < 0.05), while no significant change was found in the VitD levels. Conclusion Physical exercises, especially the endurance feature of the training modality, could increase serum FGF23 and s-Klotho levels and decrease FBG and HbA1c levels in postmenopausal T2DM women which might be a sign of improvement in glucose metabolism through regulation of VitD-FGF23-s-klotho axis.