The purpose of this study was to identify how generalized fatigue along with hormonal changes throughout the menstrual cycle affects trunk variability and local dynamic stability during gait. General fatigue was induced by an incremental test on a treadmill, and the menstrual cycle was divided into three phases: follicular, ovulatory, and luteal. Twenty-six healthy, young volunteers (aged 18 to 28 years) who did not use oral contraceptives or other hormonal drugs with a regular menstrual cycle participated in the study. They walked on the treadmill for 4 min at the preferred speed, before the incremental test, followed by four sets of 4 min alternating between walking, also at preferred speed, and resting. From trunk kinematic data, the following were extracted: the mean of the standard deviation along strides, as a measure of variability, and the maximum Lyapunov exponent, as a measure of local dynamic stability (LDS). After the incremental test, variability increased, and LDS decreased. However, they showed a tendency to return to the initial value faster in women compared to previous results for men. In the follicular phase, which has less hormonal release, the volunteers had an almost complete recovery in LDS soon after the first rest interval, suggesting that female hormones can interfere with fatigue recovery. Nevertheless, concerning the LDS, it was significantly lower in the luteal phase than in the follicular phase. Women that are not taking oral contraceptives should be aware that they are susceptible to increased gait instabilities in the pre-menstrual phase after strenuous activities.