It is generally accepted that local muscular fatigue can negatively affect position sense. Interestingly, it has been proposed that in women, position sense and neuromuscular coordination may be affected by fluctuations of estrogen and progesterone levels. The aim of this study was to examine the possible effect of localized muscle fatigue on knee joint position sense at two phases of the menses: follicular and luteal. Twenty physically active females aged 19–30 years, with normal menses, volunteered for this study. An isokinetic dynamometer was used to evaluate proprioception and perform the fatigue protocol of the knee extensors and flexors. Knee proprioception at rest and after fatigue at three knee target angles (30°, 45°, 60°) was measured. A three-way ANOVA analysis with repeated measures was performed. The results showed that the main effect of fatigue was significant, but no main effect of the menstrual cycle phase was found. Additionally, a main effect was found for the target angle (more flexed target knee joint angles were associated with larger angular error deviations). In conclusion, localized muscle fatigue can significantly reduce the accuracy of active knee joint repositioning in both the luteal and the follicular menstrual phases in young, physically active healthy women.