CONTEXT: The supplementary motor area (SMA) is involved in the functional deficits of chronic ankle instability (CAI), but the structural basis of its abnormalities remains unclear. OBJECTIVES: To determine the differences in volume- and surface-based morphologic features of the SMA between patients with CAI and healthy controls and the relationship between these features and the clinical features of CAI. DESIGN: Cross-sectional study. SETTING: Sports medicine laboratory. PATIENTS OR OTHER PARTICIPANTS: A total of 32 patients with CAI (10 women, 22 men; age = 32.46 ± 7.51 years) and 31 healthy controls (12 women, 19 men; age = 29.70 ± 8.07 years) participated. MAIN OUTCOME MEASURE(S): We performed T1-weighted structural magnetic resonance imaging of participants and calculated volume- and surface-based morphologic features of SMA subregions. These subregions included anterior and posterior subdivisions of the medial portion of Brodmann area 6 (6 ma and 6 mp, respectively) and supplementary and cingulate eye fields. Between-group comparisons and correlation analysis with clinical features of CAI were performed. RESULTS: Moderately thinner 6 mp (motor-output site; Cohen d = -0.61; 95% CI = -1.11, -0.10; P = .02) and moderately plainer 6 ma (motor-planning site; Cohen d = -0.70; 95% CI = -1.20, -0.19; P = .01) were observed in the CAI than the control group. A thinner 6 mp was correlated with lower Foot and Ankle Ability Measure Activities of Daily Living subscale scores before (r = 0.400, P = .02) and after (r = 0.449, P = .01) controlling for covariates. CONCLUSIONS: Patients with CAI had a thinner 6 mp and a plainer 6 ma in the SMA compared with controls. The thin motor-output site of the SMA was associated with ankle dysfunction in patients. This morphologic evidence of maladaptive neuroplasticity in the SMA might promote more targeted rehabilitation of CAI.