Abstract High levels of alexithymia, a personality trait closely associated with emotion dysregulation, have been found in several psychiatric disorders including borderline personality disorder (BPD). Both BPD and alexithymia have been related to impaired cortical inhibition; however, this relationship has not been tested directly. The aim of the present study was, therefore, to investigate whether cortical inhibition is modulated by alexithymia in BPD. Fifteen BPD patients with Toronto-Alexithymia Scale (TAS-20) scores ≥61, 14 BPD patients with TAS-20 <61, and 16 healthy controls were examined using different TMS paradigms. High-alexithymia patients showed a shortened cortical silent period (CSP) compared to low-alexithymia patients and controls. Additionally, a significant inverse correlation was found between the TAS-20, the left CSP and the left transcallosal conduction time. These findings indicate that alexithymia is associated with changes in GABAergic neurotransmission and facilitated transcallosal inhibition. The results highlight the importance of considering alexithymia in BPD.