An often-overlooked comorbidity of type 2 diabetes (T2D) is increased fracture risk. Since traditional T2D therapies focus solely on glucose homeostasis, there is an increased need for effective treatment strategies that improve both metabolic and bone health. The current study evaluated if previously reported protective effects of exercise (EX) on cortical bone geometry and biomechanical properties are due to the prevention of obesity compared with obese Otsuka Long-Evans Tokushima Fatty (OLETF) rats or the unique skeletal effects of exercise. Four-week-old male OLETF rats were randomly assigned to 1 of 3 groups, each fed a standard rodent chow diet until 40 weeks of age: ad libitum-fed sedentary (O-SED), ad libitum-fed EX (O-EX), or a control group body-weight−matched to the O-EX group by caloric restriction (O-CR). Ad libitum-fed sedentary Long-Evans Tokushima Otsuka (L-SED) rats were used as a lean control. EX or CR prevented the excess body mass accumulation and elevated HbA1c observed in O-SED. Total-body bone mineral density was greater in O-EX than O-CR, but similar to L-SED and O-SED. O-EX and O-CR had lower osteocalcin and TRAP5b than O-SED and L-SED. EX or CR prevented the ∼3-fold increase in CTx in O-SED versus L-SED. EX increased femoral cortical mass accumulation and expansion at the mid-diaphysis compared with O-CR. EX or CR significantly increased tissue-level stiffness and strength compared with O-SED and L-SED, but O-EX had greater whole-bone stiffness than all other groups. In summary, EX has distinct advantages over CR for improving bone biomechanical properties in hyperphagic OLETF rats.