The aim of this study was to follow the circadian fluctuation of the spontaneous pedal rate and the motor spontaneous tempo (MST) in a sample of highly trained cyclists. Ten subjects performed five test sessions at various times of day. During each test session, subjects were required to perform (i) a finger-tapping task, in order to set the MST and (ii) a submaximal exercise on a cycle ergometer for 15 min at 50% of their Wmax. For this exercise, pedal rate was freely chosen. Spontaneous pedal rate and heart rate (HR) were measured continuously. The results demonstrated a circadian variation for mean oral temperature, HR, and MST. Under submaximal exercise conditions, HR showed no significant time-of-day influence although spontaneous pedal rate changed significantly throughout the day. Circadian rhythm of oral temperature and pedal rate were strongly correlated. Moreover, a significant positive correlation was found between MST and pedal rate. Both parameters may be controlled by a common brain oscillator. MST, rest HR, and pedal rate changes follow the rhythm of internal temperature, which is considered to be the major marker in chronobiology, therefore, if there is a relation between MST and pedal rate, we cannot rule out partial dependence of both parameters on body temperature.