Progressive balance exercises may change corticomotor excitability during the learning process of postural stability control. The primary purpose of the present study was to assess corticomotor excitability corresponding to the peroneus longus muscle under transcranial magnetic stimulation following 6 weeks of progressive balance exercises in individuals suffering from functional ankle instability. Eligible volunteers with functional ankle instability were randomly and equally assigned to either the intervention or control groups. The intervention group participated in progressive balance exercises every other day for 6 weeks, while the control group continued their daily activities and refrained from new physical activities. The variables were measured in the intervention group before and after the progressive balance exercises, and in the control group twice at an interval of 6 weeks. The primary variables included the active and resting corticomotor thresholds, motor evoked potential, and cortical silent period, which were measured using an electromyography device under a transcranial magnetic stimulator. The corticomotor thresholds and cortical silent period of the peroneus longus muscle significantly decreased in the intervention group following progressive balance exercises (p-value < 0.001), whereas the normalized motor evoked potential significantly increased in the same group (p-value < 0.001). Conversely, no significant changes were detected in the control group (p-value > 0.086). The present study revealed, for the first time, that 6 weeks of progressive balance exercises significantly increased corticomotor excitability corresponding to the peroneus longus muscle and improved balance control in individuals suffering from functional ankle instability.