Humans perform rhythmic, locomotor movements with the arms and legs every day. Studies using reflexes to probe the functional role of the CNS suggest that spinal circuits are an important part of the neural control system for rhythmic arm cycling and walking. Here, by studying motor evoked potentials (MEPs) in response to transcranial magnetic stimulation (TMS) of the motor cortex, and H-reflexes induced by electrical stimulation of peripheral nerves, we show a reduction in corticospinal excitability during rhythmic arm movement compared with tonic, voluntary contraction. Responses were compared between arm cycling and tonic contraction at four positions, while participants generated similar levels of muscle activity. Both H-reflexes and MEPs were significantly smaller during arm cycling than during tonic contraction at the mid-point of arm-flexion (F = 13.51, p = 0.006; F = 11.83, p = 0.009). Sub-threshold TMS significantly facilitated the FCR H-reflex during tonic contractions, but did not significantly modulate H-reflex amplitude during arm cycling. The data indicate a reduction in the responsiveness of cells comprising the fast, monosynaptic, corticospinal pathway during arm cycling, and suggest that the motor cortex may contribute less to motor drive during rhythmic arm movement than during tonic, voluntary contraction. Our results are consistent with the idea that sub-cortical regions contribute to the control of rhythmic arm movements despite highly developed corticospinal projections to the human upper limb.