The aim was to compare lean and overweight females in regard to the effects of eccentric exercise on muscle damage indices, resting energy expenditure (REE) and respiratory quotient (RQ) as well as blood lipid and lipoprotein profile. Lean and overweight females (deviated by their body mass index) performed an eccentric exercise session. Muscle damage, energy cost and lipid profile were assessed pre-exercise and up to 72 h post-exercise. After eccentric exercise (i) muscle damage indices were affected more in the overweight subjects compared with the lean subjects; (ii) the elevation of absolute and relative REE was larger and more prolonged in the overweight group compared with the lean group; (iii) after 24 h, RQ had significantly declined, with the overweight subjects exhibiting a larger reduction compared with the lean group; and (iv) the blood lipid profile was favorably modified, with the overweight group exhibiting more favorable responses compared with the lean group. The differences between the lean and the overweight subjects may be partly due to the fact that overweight individuals experienced greater muscle damage than lean individuals. Eccentric exercise may be a promising lifestyle factor to combat obesity and dyslipidemias.