The purpose of this study was to compare the prevalence and implications of expiratory flow limitation (EFL) during exercise in boys and girls. Forty healthy, prepubescent boys (B; n = 20) and girls (G; n = 20) were tested. Subjects completed pulmonary function tests and an incremental cycle maximal oxygen uptake (V̇o_2max) test. EFL was recorded at the end of each exercise stage using the % tidal volume overlap method. Ventilatory and metabolic data were recorded throughout exercise. Arterial oxygen saturation (Sp_O2) was determined via pulse oximetry. Body composition was determined using dual-energy X-ray absorptiometry. There were no differences (P > 0.05) in height, weight, or body composition between boys and girls. At rest, boys had significantly higher lung volumes (total lung capacity, B = 2.6 ± 0.5 liters, G = 2.1 ± 0.5 liters) and peak expiratory flow rates (B = 3.6 ± 0.6 l/s; G = 1.6 ± 0.3 l/s). Boys also had significantly higher V̇o_2max (B = 46.9 ± 5.9 ml·kg lean body mass⁻¹·min⁻¹, G = 41.7 ± 6.6 ml·kg lean body mass⁻¹·min⁻¹) and maximal ventilation (B = 49.8 ± 8.8 l/min, G = 41.2 ± 8.3 l/min) compared with girls. There were no sex differences (P > 0.05) at V̇o_2max in VE /Vco₂, end-tidal Pco₂, heart rate, respiratory exchange ratio, or Sp_O2. The prevalence (B = 19/20 vs. G = 18/20) and severity (B = 58 ± 7% vs. G = 43 ± 8% tidal volume) of EFL was not significantly different in boys compared with girls at V̇o_2max. A significant relationship existed between % EFL at V̇o_2max and the change in end-expiratory lung volume from rest to maximal exercise in boys (r = 0.77) and girls (r = 0.75). In summary, our data suggests that EFL is highly and equally prevalent in prepubescent boys and girls during heavy exercise, which led to an increased end-expiratory lung volume but not to decreases in arterial oxygen saturation.