The borderline personality disorder (BPD) is characterized by a severe pattern of instability in emotional regulation, interpersonal relationships, identity and impulse control. These functions are related to the prefrontal cortex (PFC), and since PFC shows a rich anatomical connectivity with the cerebellum, the functionality of the cerebellar-PFC axis may impact on BPD. In this study, we investigated the potential involvement of cerebello-thalamo-cortical connections in impulsive reactions through a pre/post stimulation design. BPD patients (n = 8) and healthy controls (HC; n = 9) performed an Affective Go/No-Go task (AGN) assessing information processing biases for positive and negative stimuli before and after repetitive transcranial magnetic stimulation (rTMS; 1 Hz/10 min, 80% resting motor threshold (RMT) over the left lateral cerebellum. The AGN task consisted of four blocks requiring associative capacities of increasing complexity. BPD patients performed significantly worse than the HC, especially when cognitive demands were high (third and fourth block), but their performance approached that of HC after rTMS (rTMS was almost ineffective in HC). The more evident effect of rTMS in complex associative tasks might have occurred since the cerebellum is deeply involved in integration and coordination of different stimuli. We hypothesize that in BPD patients, cerebello-thalamo-cortical communication is altered, resulting in emotional dysregulation and disturbed impulse control. The rTMS over the left cerebellum might have interfered with existing functional connections exerting a facilitating effect on PFC control.