Purpose: To investigate the effect of the menstrual cycle (MC) on exercise performance across the power-duration relationship (PDR). We hypothesized females would exhibit greater variability in the PDR across the MC than males across a similar timespan, with critical power (CP) and Work-prime (W') being lower during the early follicular phase than the late follicular and mid-luteal phases. Methods: Seven eumenorrheic, endurance-trained female adults performed multiple constant-load-to-task-failure and maximum-power tests at three time points across the MC (early follicular, late follicular, mid-luteal phases). Ten endurance-trained male adults performed the same tests approximately 10 days apart. Results: No differences across the PDR were observed between MC phases (CP: 186.74 ± 31.00 W, P = 0.955, CV = 0.81 ± 0.65 %) (W': 7,961.81 ± 2,537.68 J, P = 0.476, CV = 10.48 ± 3.06 %). CP was similar for male and female subjects (11.82 ± 1.42 W • kg−1 vs. 11.56 ± 1.51 W • kg−1, respectively) when controlling for leg lean mass. However, W' was larger (P = 0.047) for male subjects (617.28 ± 130.10 J • kg−1) than female subjects (490.03 ± 136.70 J • kg−1) when controlling for leg lean mass. Conclusion: MC phase does not need to be controlled when conducting aerobic endurance performance research on eumenorrheic female subjects without menstrual dysfunction. Nevertheless, several sex differences in the power-duration relationship exist, even after normalizing for body composition. Therefore, previous studies describing the physiology of exercise performance in male subjects may not perfectly describe that of female subjects.