Ischemic cerebellar infarctions produce distinct clinical patterns including motor disturbances such as limb dysmetria, intention tremor, axial lateropulsion, and dysarthria. Repetitive transcranial magnetic stimulation (rTMS) might serve as an innovative tool to support functional recovery in stroke patients but has never been tested in patients with cerebellar stroke. The aim of the present study was to determine if excitatory repetitive transcranial magnetic stimulation protocol the “intermittent theta burst stimulation” (iTBS) applied over the lateral cerebellum on patients affected by cerebellar stroke could influence the plasticity of the cerebello-thalamo-cortical-circuits. Six chronic cerebellar stroke patients were submitted to two weeks of iTBS applied bilaterally over the cerebellum. All patients underwent magnetic resonance imaging (MRI) at 3T including T1-weighted volumes to reconstruct for each patient the damaged area. Before and after the iTBS treatment all patient were evaluated by the Modified International Cooperative Ataxia Rating Scale (MICARS), an useful tool for assessing and monitoring cerebellar motor function. Moreover, we explored the functional connectivity between the cerebellar hemisphere and the contralateral motor cortex (CBI), the intra-cortical inhibition (SICI) and intra-cortical facilitation (ICF) by means of paired-pulse TMS. We found that after two weeks of cerebellar iTBS was a decreased CBI at ISI = 5 ms and induced an increase of ICF at ISI = 15 ms. These neurophysiological changes were paralleled by clinical improvement as assessed by the MICARS scale. Among the sub-scales of the MICARS patients reported a clinical improvement ( p = 0.02 at t -test) of the posture and gait items, but not in the kinetic functions, speech disorders or oculomotor items. These preliminary results provide novel evidence that cerebellar TBS can be used to promote functional recovery of patients with cerebellar stroke. These clinical improvement could be related to long-lasting changes in the excitability of cerebello-thalamo-cortical pathways.