We tested whether expiratory flow limitation (EFL) occurs in endurance athletes in a moderately hypobaric hypoxic environment equivalent to 2500 m above sea level and, if so, whether EFL inhibits peak ventilation (V˙Epeak), thereby exacerbating the hypoxia‐induced reduction in peak oxygen uptake (V˙O2peak). Seventeen young male endurance runners performed incremental exhaustive running on separate days under hypobaric hypoxic (560 mmHg) and normobaric normoxic (760 mmHg) conditions. Oxygen uptake (V˙O2), minute ventilation (V˙E), arterial O2 saturation (SpO2), and operating lung volume were measured throughout the incremental exercise. Among the runners tested, 35% exhibited EFL (EFL group, n = 6) in the hypobaric hypoxic condition, whereas the rest did not (Non‐EFL group, n = 11). There were no differences between the EFL and Non‐EFL groups for V˙Epeak and V˙O2peak under either condition. Percent changes in V˙Epeak (4 ± 4 vs. 2 ± 4%) and V˙O2peak (−18 ± 6 vs. −16 ± 6%) from normobaric normoxia to hypobaric hypoxia also did not differ between the EFL and Non‐EFL groups (all P > 0.05). No differences in maximal running velocity, SpO2, or operating lung volume were detected between the two groups under either condition. These results suggest that under the moderate hypobaric hypoxia (2500 m above sea level) frequently used for high‐attitude training, ~35% of endurance athletes may exhibit EFL, but their ventilatory and metabolic responses during maximal exercise are similar to those who do not exhibit EFL.