In contrast to other rhythmic tasks such as running, the preferred movement rate in cycling does not minimize energy consumption. It is possible that neurophysiological mechanisms contribute to the choice of cadence, however this phenomenon is not well understood. Eleven participants cycled at a fixed workload of 125 W and different cadences including a freely chosen cadence (FCC, ~72), and fixed cadences of 70, 80, 90 and 100 revolutions per minute (rpm) during which transcranial magnetic stimulation (TMS) was used to measure short interval intracortical inhibition (SICI) and intracortical facilitation (ICF). There was significant increase in SICI at 70 (P = 0.004), 80 (P = 0.008) and 100 rpm (P = 0.041) compared to FCC. ICF was significantly reduced at 70 rpm compared to FCC (P = 0.04). Inhibition-excitation ratio (SICI divided by ICF) declined (P = 0.014) with an increase in cadence. The results demonstrate that SICI is attenuated during FCC compared to fixed cadences. The outcomes suggest that the attenuation of intracortical inhibition and augmentation of ICF may be a contributing factor for FCC.