Fatigue can impair function of the three sensory systems (vestibular, visual, and somatosensory) that control postural balance. Yet impairment may be greater among individuals with than those without chronic ankle instability (CAI). The present study used posturography assessment to extend previous findings demonstrating reduced function of the three systems in CAI participants following fatigue. Our aim in this study was to examine the influence of anaerobic and aerobic protocols on the function of these three sensory systems in individuals with and without CAI. We assessed 60 healthy physical education students ( Mage = 24.3, SD = 3.4) by a Tetrax® Posturography device for Stability-Index and Fourier-frequencies [ low sway (F1) visual input, medium-low sway (F2–F4) vestibular input, medium–high sway (F5–F6) somatosensory input] and by the Active Movement Extent Discrimination Assessment (AMEDA) for active ankle somatosensory ability, before and after performing anaerobic or aerobic protocols. Among participants, 45% were identified with CAI. We found significant Time effect (pre-post), CAI effect, and CAI X Time interactions for Fourier frequencies, Stability-Index, and AMEDA scores, indicating greater pre-post deterioration for those with CAI compared to those without CAI ( p < .05). CI (95%) showed that, although there was a Time effect for F1, F2–F4, and F5–F6, only F5–F6 frequencies (i.e., somatosensory input) showed the CAI effect and the Time X CAI interaction. Thus, participants with and without CAI showed reduced visual, vestibular, and somatosensory ability following fatigue. While we found greater deterioration in both passive and active somatosensory ability (F5-6 and AMEDA) among individuals with CAI compared with those with no-CAI, we recommend intervention programs for improving vestibular abilities following fatigue in both those with and without CAI.