The aim of the present study was to compare running economy between competitive and recreational level athletes at their individual ventilatory thresholds on track and to compare body composition parameters that are related to the individual running economy measured on track. We performed a cross-sectional analysis of a total 45 male runners classified as competitive runners (CR; n = 28) and recreational runners (RR; n = 17). All runners performed an incremental test on treadmill until voluntary exhaustion and at least 48 h later a 2 × 2000 m test at indoor track with intensities according to ventilatory threshold 1, ventilator threshold 2. During the running tests, athletes wore portable oxygen analyzer. Body composition was measured with Dual energy X-ray absorptiometry (DXA) method. Running economy at the first ventilatory threshold was not significantly related to any of the measured body composition values or leg mass ratios either in the competitive or in the recreational runners group. This study showed that there was no difference in the running economy between distance runners with different performance level when running on track, while there was a difference in the second ventilatory threshold speed in different groups of distance runners. Differences in running economy between competitive and recreational athletes cannot be explained by body composition and/or different leg mass ratios.