Highly trained aerobic athletes progressively use most of their breathing reserve with increased exercise intensity during whole-body exercise. Additionally, females typically present proportionally smaller lungs than males. Therefore, sex, exercise intensity, and breathing reserve use likely influence the volume and time in which respiratory parameters vary between consecutive breaths during whole-body exercise. However, breath-by-breath variability has been scarcely investigated during exercise. Accordingly, we sought to investigate breath-by-breath pulmonary ventilation (V̇E), tidal volume (VT), and respiratory frequency (fR) variability during a maximal treadmill incremental exercise test in 17 females and 18 males highly trained professional endurance runners. The breath-by-breath variability was analyzed by root mean square of successive differences (RMSSD) within 1-minute windows. Females had lower absolute and percent predicted forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) than males, as well as lower height-adjusted absolute FVC than males. V̇E and VT reserve use were similar between the sexes at peak exercise. While RMSSDV̇E and RMSSDfR did not change over exercise (P > 0.05), RMSSDVT progressively decreased (P < 0.001). RMSSDVT was negatively correlated with VT reserve use only in males. Females showed lower RMSSDV̇E than males during the entire exercise test (P < 0.001). At iso-V̇E reserve use, between-sex differences in RMSSDV̇E persisted (P = 0.003). Our findings indicate that exercise intensity decreases VT variability in professional runners, which is linked to VT reserve use in males but not females. Additionally, the female sex lowers V̇E variability regardless of exercise intensity and V̇E reserve use.