Study aim: running economy (RE) is important indicator of endurance performance. During puberty dynamic changes in body composition and function are observed, as such RE is also expected to change. The aim of the study was to compare the running economy (RE) in overweight and normoweight boys during a running exercise performed with constant velocity, and the assessment of changes in RE during puberty. Material and methods: the RE of the subjects was evaluated twice: at the age of 11–12 and two years later. 18 overweight and 17 normal weight boys performed a graded test and a week later a submaximal run on a mechanical treadmill. During the exercise, physiological variables (oxygen uptake, heart rate, pulmonary ventilation, tidal volume and breathing frequency) were measured. Results: the intensity of work in both tests (%VO2max, %HRmax) was significantly higher in the overweight boys and decreased with age (non significantly) in both groups. The physiological response during the run in the overweight boys was significantly higher compared to normal weight. When the oxygen uptake was expressed as VO2.BM–0.75, the RE was similar in normal weight and overweight boys. During puberty, the inter-group differences in the metabolic cost of work stay at a relatively stable level. Conclusions: the lowered endurance performance in the overweight boys during puberty remains unchanged. The changes in physiological variables during puberty in both groups occurred in a similar way – the body composition did not influence the course of these changes in puberty.