Motor imagery (MI) is the mental simulation of an action without any overt movement. Functional evidences show that brain activity during MI and motor execution (ME) largely overlaps. However, the role of the primary motor cortex (M1) during MI is controversial. Effective connectivity techniques show a facilitation on M1 during ME and an inhibition during MI, depending on whether an action should be performed or suppressed. Conversely, Transcranial Magnetic Stimulation (TMS) studies report facilitatory effects during both ME and MI. The present TMS study shed light on MI mechanisms, by manipulating the instructions given to the participants. In both Experimental and Control groups, participants were asked to mentally simulate a finger-thumb opposition task, but only the Experimental group received the explicit instruction to avoid any unwanted fingers movements. The amplitude of motor evoked potentials (MEPs) to TMS during MI was compared between the two groups. If the M1 facilitation actually pertains to MI per se, we should have expected to find it, irrespective of the instructions. Contrariwise, we found opposite results, showing facilitatory effects (increased MEPs amplitude) in the Control group and inhibitory effects (decreased MEPs amplitude) in the Experimental group. Control experiments demonstrated that the inhibitory effect was specific for the M1 contralateral to the hand performing the MI task and that the given instructions did not compromise the subjects’ MI abilities. The present findings suggest a crucial role of motor inhibition when a “pure” MI task is performed and the subjects are explicitly instructed to avoid overt movements. •TMS studies found facilitatory effects on primary motor cortex during Motor imagery.•Contrariwise, effective connectivity on fMRI data shows inhibitory effects.•In this TMS study, we isolated the MI function from its subliminal EMG activity.•When a “pure” MI is performed, a crucial role of motor inhibition was found.•This nullifies the conflict between TMS and other neurophysiological techniques.