Essential blepharospasm (BEB) is a focal dystonia characterized by abnormal brainstem excitability and impaired inhibitory control within trigeminal–facial circuits. Botulinum toxin type A (BoNT-A) is the established first-line treatment, primarily acting at the neuromuscular junction. However, whether BoNT-A also modulates central brainstem circuits in BEB patients remains unclear, and dedicated neurophysiological studies have yielded conflicting results. To investigate whether BoNT-A modulates brainstem interneuronal excitability in BEB using the blink reflex recovery cycle and to correlate clinical outcomes with neurophysiological results. Thirteen patients with BEB underwent neurophysiological and clinical evaluation before (T0) and one month after (T1) BoNT-A treatment. The blink reflex recovery cycle was assessed at interstimulus intervals (ISIs) of 200, 300, 500, and 1000 ms. Clinical severity was assessed using the BSPSS, JRS, and BDS scales. The R2 amplitude ratio showed a statistically significant decrease after treatment across all ISIs (all p ≤ 0.001), indicating reduced brainstem interneuronal excitability. All clinical scales demonstrated statistically significant improvement after treatment (BSPSS, JRS, BDS; all p < 0.001). This pilot study provides preliminary evidence that BoNT-A treatment may reduce brainstem interneuronal excitability in BEB patients, as evidenced by a substantial and consistent decrease in R2 amplitude ratios of the blink reflex recovery cycle. These findings are consistent with a central modulatory effect of BoNT-A beyond its established peripheral action. Larger controlled studies are warranted to confirm these results.