Introduction: Army training often incurs physical injury, with ankle injuries occurring in 10-20 % of soldiers during training. These patterns are reported with similar frequency and body-part distribution of injury in Israeli Defence Force (IDF) combat units. Research has shown that 32 % of individuals with ankle injuries develop chronic ankle instability (CAI). This study aimed to determine whether having chronic ankle instability (CAI) affects the physical performance of soldiers during their army training, as measured in routine army fitness tests, and in other neuromuscular tests. It was hypothesised that soldiers with CAI would not perform as well on all lower limb performance tests, and would improve less during the period of military training. Methods: A prospective cohort comparison was made within soldiers undertaking the Infantry Commanders Course (IC Course) of the IDF. Soldiers were tested at weeks one and 14 of the course, including with a 3,000m timed run, an agility test over an X-shaped course, the Y Balance Test (YBT) and the Active Movement Extent Discrimination Assessment (AMEDA) somatosensory test. All participants completed the required physical training throughout the course. Changes in physical performance were analysed using a two-way ANOVA, for soldier groups categorised as having healthy ankles or CAI based on a score of ≤25 on the Cumberland Ankle Instability Tool (CAIT) questionnaire. Results: 105 soldiers (mean (±SD) height 1.75m ± 0.06, weight 75.15kg ± 10.74) participated and were separated into those with and without CAI (n=59 and 46, respectively). Overall, scores on all 4 tests (3,000 m run, X-agility test, YBT and AMEDA) improved during the course. However, soldiers with CAI did not improve on the X-agility test, while those with healthy ankles did. At the start of the course, soldiers with CAI performed worse on the YBT-PM (postero-medial direction), but this difference was no longer present at 14 weeks. Compared with their healthy counterparts, soldiers with CAI performed better on the AMEDA at the start and 14 -week testing points. Discussion: Ankle instability restricts agility gains in soldiers during 14-weeks of physical training but has no effect on 3,000m running performance. Soldiers with CAI perform worse in YBT balance tests, in the Anterior and PM directions particularly. Soldiers with CAI have better somatosensory acuity than those with stable ankles, despite the CAI association with worse performance in other tests. This heightened somatosensory awareness may enable them to compensate for lower performance in other tests. Conflict of interest statement: “This study was supported by a research grant from the Medical Research Directorate of the Israeli Defence Forces. No other specific grant funding was received from agencies in the public, commercial, or not-for-profit sectors.”