Studies using force-matching tasks have suggested that when we feel a “sense of effort,” cortical regions may act to increase motor commands, and thus recruit additional motor units, in order to compensate for the exerted force. We hypothesized that suppressing activity in the primary motor cortex (M1), which is the source of the motor commands, would initiate the same process, and induce the same sense of effort. In a force-matching task, grip force was applied to ‘right’ hand and 10 healthy participants were asked to try to exert the same amount by using ‘left’ hand, with no visual feedback. On some trials, low-frequency, repetitive transcranial magnetic stimulation (lf-rTMS) was used to suppress the M1 and the primary somatosensory cortex (SI) in the left hemisphere, separately. Results showed that participants tended to overestimate the level of exerted force by up to 24%. In contrast, sham stimulation of the M1 and lf-rTMS over the SI did not significantly affect participants’ estimations. Further, the M1 suppression resulted in a 42% reduction in motor-evoked potentials. Thus, the M1 suppression can affect our sense of effort, suggesting that compensatory neural mechanisms that increase the MI activity may play an important role in producing senses of effort.