Key points  Theta burst stimulation (TBS) protocols of repetitive transcranial magnetic stimulation (rTMS) have after‐effects on excitability of motor areas thought to be due to LTP‐ and LTD‐like processes at cortical synapses. TBS protocols have significant advantages over other rTMS techniques in time and intensities used. Eyeblink classical conditioning (EBCC) is a form of associative motor learning in which paired presentation of a conditioned (CS) and unconditioned stimulus (US) leads to the production of a conditioned eyeblink response (CR). EBCC, with its heavy dependence on cerebellar function, is an ideal protocol with which to assess and potentially quantify the possible influence of TBS on the cerebellum. We show that cerebellar TBS has clear effects on EBCC in humans, providing evidence that TBS can influence cerebellar function despite the low intensities of stimulation used and the anatomical constraints of the posterior fossa.