Repetitive transcranial magnetic stimulation (rTMS) can induce short-term reorganisation of human motor cortex. Here, we investigated the effect of rTMS during relaxation and weak voluntary muscle contraction on motor cortex excitability and hand function. Subjects (n=60) participated in one of four studies. Single transcranial magnetic stimuli were delivered over the motor area of the first dorsal interosseus for measurement of motor evoked potential (MEP) size before and after real or sham rTMS delivered at an intensity of 80% of active motor threshold. rTMS involved trains of stimuli applied at 6 Hz for 5 s and repeated every 30 s for 10 minutes. Resting MEP size was suppressed for 15 mins after rTMS during relaxation. However, MEP suppression was abolished when additional brief voluntary contractions were performed before and after rTMS (Study one). Resting MEP size was suppressed for 30 mins after rTMS during weak voluntary contraction. MEP suppression was present even though voluntary contractions were performed before and after rTMS (Study two). The MEP suppression most likely reflects a decrease in motor cortical excitability. Surprisingly, rTMS during voluntary contraction did not alter maximal finger tapping speed or performance on a Grooved Pegboard test, object grip and lift task (Study three), and visuomotor tracking task (Study four). These studies document the complex relationship between voluntary movement and rTMS-induced plasticity in motor cortex. This work has implications for the optimisation of rTMS parameters for improved efficacy and potential therapeutic applications.