Environmental stimuli may acquire threat-related properties through pairing with an aversive event, and exert a powerful influence on behaviour. Nevertheless, the extent to which the human cortical motor system learns to prepare to aversive events remains largely unexplored. Here, in two experiments on two independent groups of healthy individuals (exp. 1: N=28, exp. 2: N=30) we investigated whether and how changes in corticospinal excitability mark the acquisition of threat learning. In both experiments, participants completed a Pavlovian threat learning task in which two different neutral stimuli (coloured dots) acquired threat-related value by predicting a lateralized aversive shock, either to the left (left conditioned stimulus, CS+L) or right (CS+R) arm (Exp.1) or hand (Exp.2). Another stimulus (CS-) never predicted shock. Electrodermal activity (SCR) was collected to characterize changes in autonomic response between CSs. Critically, changes in corticospinal excitability were assessed by acquisition of motor-evoked potentials (MEP) recorded from two right hand and arm muscles (FDI and ECR muscles, respectively), and elicited by transcranial magnetic stimulation (TMS) applied to the left primary motor cortex. We found increased SCR for CS+R and CS+L compared with CS-, which did not distinguish the laterality of impending shock. In contrast, a lateralized inhibitory effect emerged for corticospinal excitability. Indeed, we found a reduction in the FDI MEP amplitude for CS+R, compared with CS+L and CS-. By tracking the development of the conditioned corticospinal response, we then revealed that the presentation of a conditioned stimulus triggers corticospinal inhibition in anticipation of the delivery of a noxious somatosensory outcome, which is mapped relative to the body part where the outcome is expected. This work advances the mechanistic understanding of Pavlovian learning and threat anticipation, showing that a motor representation of the outcome is part of the learning content, even though the outcome occurs unconditional to any overt motor response.