The aim of this study was to compare bone variables in active overweight/obese men and sedentary overweight/obese men. Thirty-seven active overweight/obese men and 45 sedentary overweight/obese men participated in this study. Weight and height were measured, and body mass index was calculated. Body composition and bone variables (bone mineral content [BMC], bone mineral density [BMD], geometric indices of hip bone strength, and trabecular bone score) were measured by DXA. Physical activity level, daily calcium intake, daily protein intake, and sleep duration were measured by validated questionnaires. Maximum oxygen consumption (VO2 max) was determined by direct measurement while exercising on a medical treadmill. One-repetition-maximum half-squat of the lower limbs was measured using a validated protocol. Body weight and body mass index were higher in sedentary overweight/obese men than in active overweight/obese men. In the whole population (n = 82), VO2 max (in liter per minute), lean mass, and one-repetition-maximum half-squat were positively correlated to BMC, BMD, and geometric indices of hip bone strength (cross-sectional area and section modulus [Z] of the femoral neck [FN]). After adjusting for body weight using a 1-way analysis of covariance, active overweight/obese men displayed higher whole-body BMC, lumbar spine BMD, total hip BMD, FN BMD, FN cross-sectional area, and FN Z values than sedentary overweight/obese men. In conclusion, the current study suggests that physical activity level positively affects bone variables in overweight/obese men. Optimizing lean mass and muscular strength of the lower limbs can help to prevent osteoporosis in overweight and obese men.