Many athletes with recurrent ankle sprains complain of neurophysiological deficits related to chronic ankle instability (CAI). However, it remains unclear how changes in the corticospinal pathway affect the potential risk of subsequent ankle sprains. The purpose of this study was to investigate whether the corticospinal excitability (input-output properties) and silent period (SP) could be related to the risk of subsequent ankle sprains among athletes. Forty-three male collegiate basketball athletes were enrolled, and 82 ankles were finally sorted into four ankle groups based on symptoms (CAI, sub-CAI, copers, and normal). The neurophysiological data was recorded in both ankles using transcranial magnetic stimulation (TMS) as baseline assessments. Subsequently, we prospectively followed the occurrence of subsequent ankle sprain injuries for 24 months (SG, subsequent ankle sprain group; NSG, non-sprain group). In the baseline assessment, we confirmed that the threshold of the input-output properties in the CAI group was higher than those in the normal group. After the follow-up, 22 ankles sustained subsequent ankle sprains (SGs). We also found that SGs exhibited a significantly longer SP at the middle and high stimulus intensities of TMS compared to NSGs (60 ankles) (middle: p = 0.012, Cohen's d = 0.644, and high: p = 0.020, Cohen's d = 0.590). These findings suggest that a prolonged SP could be a crucial factor affecting subsequent ankle sprains in athletes. To prevent further recurrent sports injuries, neurophysiologic probes, particularly a longer SP, might be a potential assessment tool to return to the field.