The objective of this systematic review with meta-analysis was to determine alterations in spinal and corticospinal excitability of ankle muscles in patients with chronic ankle instability (CAI) compared to uninjured controls. Independent researchers performed comprehensive literature searches of electronic databases and included studies that compared groups with and without CAI and investigated neural excitability with Hoffmann reflex (H-reflex) and/or transcranial magnetic stimulation (TMS). A fixed-effect meta-analysis was conducted to determine group differences for (1) soleus and fibularis maximal H-reflex (Hmax)/maximal M-wave (Mmax)-ratios, and (2) soleus and fibularis longus cortical motor thresholds (CMTs). Seventeen studies were included in the current meta-analysis. They showed that the Hmax/Mmax-ratios of the soleus and the fibularis longus in the CAI group were significantly lower than those in the uninjured control group (soleus: d = −0.41, p < 0.001; fibularis longus: d = −0.27, p = 0.04). There was no evidence for changes in the CMT. This systematic review is the first to demonstrate evidence that patients with CAI present decreased spinal reflex excitability in the soleus and fibularis longus. However, there is no evidence of changes in supraspinal excitability when considering only the CMT. The latter result needs to be interpreted with caution as all except one study demonstrate some changes at the supraspinal level with CAI.